From daniel.antony.pass at googlemail.com Fri Aug 1 06:41:07 2014 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Fri, 1 Aug 2014 11:41:07 +0100 Subject: [Bio-Linux] Fwd: Announcing the NERC Environmental Omics Conference In-Reply-To: References: Message-ID: As you may have seen from our new website, the Bio-Linux project is now allied with the EOS centre, so we hope some on this list will be interested in our annual iEOS conference. Apologies if you have already received this email however there is likely to be some overlap on mailing lists. The second year of the NERC international Environmental Omics Synthesis Conference (iEOS2014) will be taking place in Liverpool (UK), 15th-18th September, which aims to bring together Environmental researchers who are involved or interested in utilising the latest in -omic technologies. There is more information below, or at the website http://environmentalomics.org/ieos2014/ iEOS2014 is a broad spectrum conference with sessions on *Evolutionary genomics, Meta-omic analysis of biome composition and function, Archaeological omics, Epigenetic basis of phenotypic plasticity underpinning acclimatisation and Systems ecotoxicology. *More information on the agenda can be found at http://environmentalomics.org/ieos2014-agenda/ Global research is being showcased including international delegates from *Trinity College Dublin, Pennsylvania State University, US Environmental Protection Agency, University of Aberdeen, University of Sheffield, KU Leuven, Belgium, Beijing Genomics Institute (BGI) China, DKFZ (German Cancer Research Centre), Heidelberg, Ghent University Belgium, University of Massachusetts Amherst, University of Birmingham and US Army Engineer Research and Development Centre.* Complementary to the conference are fully funded workshops being ran by the NERC NBAF group on *Gene expression analysis, Metabolomics, Restriction-site Associated DNA (RAD) Data Analysis and Population genomics* . There is also a separate sponsored workshop on *"Computational Approaches to Study Biological Mechanisms: Bringing together large scale ?omics approaches and classical computational **modelling"*. There are travel and accommodation grants available for the NBAF workshops attendees. Abstract submission is still open for platform and poster presentations at the main conference. *Registration is closing on Monday 11th of August*. Platform and Poster abstracts are still accepted to that date, with a limited number of registration fellowships for PhD students that submit an abstract for a platform presentation. If this is of interest please visit the website for registration or for contact details. Additionally, please follow us via @EnvOmicsNERC for updates. ------------------------------ *iEOS2014 to be held in Liverpool in week starting 15th September 2014* *REGISTRATION EXTENDED TO FRIDAY 11TH AUGUST* *Conference Organiser: Professor F. Falciani (Chair in Integrative Systems Biology) * The conference will hosted by the Centre for Computational Biology and Modelling (CCBM) within the Institute of Integrative Biology at University of Liverpool . The aim of this conference is to bring together researchers and organisations from a range of disciplines with shared interests in the development of new approaches for data handling, generation and analysis in environmental omics. Science areas of interest include bioinformatics, DNA-barcoding, genomics, metagenomics, metabarcoding, transcriptomics, proteomics, metabolomics, epigenetics, evolutionary and ecological omics, phylogenetics, study of ancient DNA and anthropology, new tools, resources and training, and beyond as applied to the study of the natural environmental and environmentally relevant organisms and systems. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the establishment of a wider integrated ?Omic community. EOS and this conference is supported by Natural Environmental Research Council (NERC) through its Mathematics and Informatics for Environmental ?Omics Data Synthesis program and the UK Science and Technology Facilities Council (STFC) Global Challenges programme. Watch the iEOS conference page , the EOS Facebook page or follow the EOS twitter feed to keep up to date with further developments. [image: Integrative Biology University logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.molnar at sbcglobal.net Fri Aug 1 10:53:25 2014 From: s.molnar at sbcglobal.net (Stephen P. Molnar) Date: Fri, 1 Aug 2014 10:53:25 -0400 Subject: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now available Message-ID: <019a01cfad98$59d63b00$0d82b100$@molnar@sbcglobal.net> Please see the following messages. Thanks in advance. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -----Original Message----- From: Tim Booth [mailto:tbooth at ceh.ac.uk] Sent: Friday, August 01, 2014 9:40 AM To: Stephen P. Molnar Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available Hi Stephen, Glad you sorted out the shell. I'm sorry, but I can't say what might be up with the keyboard and I'm not going to start experimenting with XFCE right now as I have other priorities. You may well have more luck on the discussion mailing list: http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux Cheers, TIM On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote: > Thanks for the reply. As it turns out that was a red-faced forehead > slapping problem. After dispatching my note I realized that the shell > was zsh. > > Thanks to your reply I have successfully changed the default shell to > bash. > > There is, however anew problem, also a head scratcher for me. As I > don't like the Gnome shell and had become unenchanted with KDE, my > desktop of choice on my linux machines is XFCE, with Xfe as the file > manager of choice. I find that the keyboard doesn't seem to be > recognized by the xfwrite editor. On the other hand, nedit works as it > should. > > Your input about this problem would be much appreciated. > > Thanks in advance. > > Stephen P. Molnar, Ph.D. Life is a fuzzy set > Foundation for Chemistry Stochastic and multivariate > www.FoundationForChemistry.com > (614)312-7528 (c) > Skype: smolnar1 > > > -----Original Message----- > From: Tim Booth [mailto:tbooth at ceh.ac.uk] > Sent: Friday, August 01, 2014 5:05 AM > To: Stephen P. Molnar > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available > > Hi Stephen, > > Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so if you are a BASH fan you'll want to do: > > chsh -s /bin/bash > exec bash -l > > We do already have both L and ll aliased to that command, but not "l" > :-) > > Cheers, > > TIM > > On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote: > > I have encountered a rather strange problem with the new BioLinux v > > 8 latest. > > > > I installed the distribution in a VMware Player without any problems > > or error messages. In fact, I have a Debian v-7.6.0 distribution > > running in the same VMware device. Consequently, I have confidence > > in the virtual computer and my laptop on which it is running. > > > > I edited .bashrc to include the line alias l='ls -l --color' > > > > When I source the edited .bashrc file I get the following: > > > > computation at inga[computation] source .bashrc [ > > 2:57PM] > > .bashrc:16: command not found: shopt > > .bashrc:24: command not found: shopt > > .bashrc:108: command not found: shopt > > /usr/share/bash-completion/bash_completion:35: parse error near `]]' > > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ [ > > 2:57PM] > > > > The problem seems to be that shopt is missing! > > > > Please advise. > > > > Thanks in advance. > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy > > set > > Foundation for Chemistry Stochastic and > > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > -----Original Message----- > > From: Tim Booth [mailto:tbooth at ceh.ac.uk] > > Sent: Wednesday, July 30, 2014 11:55 AM > > To: bio-linux-announce at nebclists.nerc.ac.uk; Bio-Linux mailing list > > Subject: [Bio-linux-announce] Bio-Linux 8 now available > > > > Dear All, > > > > The Bio-Linux system gets a major new release every two years > > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS > > came out in April I've been working with help from the Bio-Linux > > community to make Bio-Linux 8 and it is now ready and available via the new website. > > > > http://environmentalomics.org/bio-linux/ > > > > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I > > encourage you all to upgrade soon, as new bioinformatics packages > > will no longer be provided for Bio-Linux 7. See the "Installation" > > section for instructions on upgrading your BL7 machine. > > > > The new Ubuntu 14.04 base system brings many benefits such as > > increased hardware compatibility and new office and multimedia > > software, but Bio-Linux itself also has many improvements and new/updated packages. > > Also for the first time there is a version in OVA format for > > VirtualBox/VMWare users, and this version will be updated whenever > > new ISO files are released. See the "What's New" and "Software List" > > pages on the website for details. > > > > As ever, please report problems and feedback to > > helpdesk at nebc.nerc.ac.uk. I can't promise to fix everything but > > will endeavour to provide help and squash bugs where I can. Also, > > please let me know if you use Bio-Linux for teaching or manage a > > large installation on your departmental server or computing lab. > > The more we can prove that people find this stuff useful, the more likely we are to get future funding! > > > > I hope you enjoy using Bio-Linux 8. > > > > TIM > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > _______________________________________________ > > Bio-Linux-announce mailing list > > Bio-Linux-announce at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From s.molnar at sbcglobal.net Sat Aug 2 14:57:11 2014 From: s.molnar at sbcglobal.net (Stephen P. Molnar) Date: Sat, 2 Aug 2014 14:57:11 -0400 Subject: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now available Message-ID: <035c01cfae83$92f592f0$b8e0b8d0$@molnar@sbcglobal.net> Please see the following messages. Thanks in advance. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -----Original Message----- From: Tim Booth [mailto:tbooth at ceh.ac.uk] Sent: Friday, August 01, 2014 9:40 AM To: Stephen P. Molnar Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available Hi Stephen, Glad you sorted out the shell. I'm sorry, but I can't say what might be up with the keyboard and I'm not going to start experimenting with XFCE right now as I have other priorities. You may well have more luck on the discussion mailing list: http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux Cheers, TIM On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote: > Thanks for the reply. As it turns out that was a red-faced forehead > slapping problem. After dispatching my note I realized that the shell > was zsh. > > Thanks to your reply I have successfully changed the default shell to > bash. > > There is, however anew problem, also a head scratcher for me. As I > don't like the Gnome shell and had become unenchanted with KDE, my > desktop of choice on my linux machines is XFCE, with Xfe as the file > manager of choice. I find that the keyboard doesn't seem to be > recognized by the xfwrite editor. On the other hand, nedit works as it > should. > > Your input about this problem would be much appreciated. > > Thanks in advance. > > Stephen P. Molnar, Ph.D. Life is a fuzzy set > Foundation for Chemistry Stochastic and multivariate > www.FoundationForChemistry.com > (614)312-7528 (c) > Skype: smolnar1 > > > -----Original Message----- > From: Tim Booth [mailto:tbooth at ceh.ac.uk] > Sent: Friday, August 01, 2014 5:05 AM > To: Stephen P. Molnar > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available > > Hi Stephen, > > Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so if you are a BASH fan you'll want to do: > > chsh -s /bin/bash > exec bash -l > > We do already have both L and ll aliased to that command, but not "l" > :-) > > Cheers, > > TIM > > On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote: > > I have encountered a rather strange problem with the new BioLinux v > > 8 latest. > > > > I installed the distribution in a VMware Player without any problems > > or error messages. In fact, I have a Debian v-7.6.0 distribution > > running in the same VMware device. Consequently, I have confidence > > in the virtual computer and my laptop on which it is running. > > > > I edited .bashrc to include the line alias l='ls -l --color' > > > > When I source the edited .bashrc file I get the following: > > > > computation at inga[computation] source .bashrc [ > > 2:57PM] > > .bashrc:16: command not found: shopt > > .bashrc:24: command not found: shopt > > .bashrc:108: command not found: shopt > > /usr/share/bash-completion/bash_completion:35: parse error near `]]' > > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ [ > > 2:57PM] > > > > The problem seems to be that shopt is missing! > > > > Please advise. > > > > Thanks in advance. > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy > > set > > Foundation for Chemistry Stochastic and > > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > -----Original Message----- > > From: Tim Booth [mailto:tbooth at ceh.ac.uk] > > Sent: Wednesday, July 30, 2014 11:55 AM > > To: bio-linux-announce at nebclists.nerc.ac.uk; Bio-Linux mailing list > > Subject: [Bio-linux-announce] Bio-Linux 8 now available > > > > Dear All, > > > > The Bio-Linux system gets a major new release every two years > > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS > > came out in April I've been working with help from the Bio-Linux > > community to make Bio-Linux 8 and it is now ready and available via the new website. > > > > http://environmentalomics.org/bio-linux/ > > > > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I > > encourage you all to upgrade soon, as new bioinformatics packages > > will no longer be provided for Bio-Linux 7. See the "Installation" > > section for instructions on upgrading your BL7 machine. > > > > The new Ubuntu 14.04 base system brings many benefits such as > > increased hardware compatibility and new office and multimedia > > software, but Bio-Linux itself also has many improvements and new/updated packages. > > Also for the first time there is a version in OVA format for > > VirtualBox/VMWare users, and this version will be updated whenever > > new ISO files are released. See the "What's New" and "Software List" > > pages on the website for details. > > > > As ever, please report problems and feedback to > > helpdesk at nebc.nerc.ac.uk. I can't promise to fix everything but > > will endeavour to provide help and squash bugs where I can. Also, > > please let me know if you use Bio-Linux for teaching or manage a > > large installation on your departmental server or computing lab. > > The more we can prove that people find this stuff useful, the more likely we are to get future funding! > > > > I hope you enjoy using Bio-Linux 8. > > > > TIM > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > _______________________________________________ > > Bio-Linux-announce mailing list > > Bio-Linux-announce at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 Stephen P. Molnar, Ph.D. Life is a fuzzy set (614)312-7528 (c) Stochastic and multivariate Skype: smolnar1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Sun Aug 3 01:40:23 2014 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 3 Aug 2014 01:40:23 -0400 Subject: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now available In-Reply-To: <53dd34a0.a9bdb40a.081c.4fc7SMTPIN_ADDED_BROKEN@mx.google.com> References: <53dd34a0.a9bdb40a.081c.4fc7SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: Hi All I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/' followed by 'sudo ./install) but getting following error. I would really appreciate if somebody help me resolve this problem. Eventually I want to upgrade to Biolinux8. Thanks Tauqeer On Sat, Aug 2, 2014 at 2:57 PM, Stephen P. Molnar wrote: > Please see the following messages. > > > > Thanks in advance. > > > > Stephen P. Molnar, Ph.D. Life is a > fuzzy set > > Foundation for Chemistry Stochastic and > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > > > -----Original Message----- > > From: Tim Booth [mailto:tbooth at ceh.ac.uk ] > > Sent: Friday, August 01, 2014 9:40 AM > > To: Stephen P. Molnar > > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available > > > > Hi Stephen, > > > > Glad you sorted out the shell. > > > > I'm sorry, but I can't say what might be up with the keyboard and I'm not > going to start experimenting with XFCE right now as I have other > priorities. You may well have more luck on the discussion mailing list: > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > Cheers, > > > > TIM > > > > On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote: > > > Thanks for the reply. As it turns out that was a red-faced forehead > > > slapping problem. After dispatching my note I realized that the shell > > > was zsh. > > > > > > Thanks to your reply I have successfully changed the default shell to > > > bash. > > > > > > There is, however anew problem, also a head scratcher for me. As I > > > don't like the Gnome shell and had become unenchanted with KDE, my > > > desktop of choice on my linux machines is XFCE, with Xfe as the file > > > manager of choice. I find that the keyboard doesn't seem to be > > > recognized by the xfwrite editor. On the other hand, nedit works as it > > > should. > > > > > > Your input about this problem would be much appreciated. > > > > > > Thanks in advance. > > > > > > Stephen P. Molnar, Ph.D. Life is a > fuzzy set > > > Foundation for Chemistry Stochastic > and multivariate > > > www.FoundationForChemistry.com > > > (614)312-7528 (c) > > > Skype: smolnar1 > > > > > > > > > -----Original Message----- > > > From: Tim Booth [mailto:tbooth at ceh.ac.uk ] > > > Sent: Friday, August 01, 2014 5:05 AM > > > To: Stephen P. Molnar > > > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available > > > > > > Hi Stephen, > > > > > > Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so > if you are a BASH fan you'll want to do: > > > > > > chsh -s /bin/bash > > > exec bash -l > > > > > > We do already have both L and ll aliased to that command, but not "l" > > > :-) > > > > > > Cheers, > > > > > > TIM > > > > > > On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote: > > > > I have encountered a rather strange problem with the new BioLinux v > > > > 8 latest. > > > > > > > > I installed the distribution in a VMware Player without any problems > > > > or error messages. In fact, I have a Debian v-7.6.0 distribution > > > > running in the same VMware device. Consequently, I have confidence > > > > in the virtual computer and my laptop on which it is running. > > > > > > > > I edited .bashrc to include the line alias l='ls -l --color' > > > > > > > > When I source the edited .bashrc file I get the following: > > > > > > > > computation at inga[computation] source .bashrc > [ > > > > 2:57PM] > > > > .bashrc:16: command not found: shopt > > > > .bashrc:24: command not found: shopt > > > > .bashrc:108: command not found: shopt > > > > /usr/share/bash-completion/bash_completion:35: parse error near `]]' > > > > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ > [ > > > > 2:57PM] > > > > > > > > The problem seems to be that shopt is missing! > > > > > > > > Please advise. > > > > > > > > Thanks in advance. > > > > > > > > Stephen P. Molnar, Ph.D. Life is a > fuzzy > > > > set > > > > Foundation for Chemistry Stochastic > and > > > > multivariate > > > > www.FoundationForChemistry.com > > > > (614)312-7528 (c) > > > > Skype: smolnar1 > > > > > > > > -----Original Message----- > > > > From: Tim Booth [mailto:tbooth at ceh.ac.uk ] > > > > Sent: Wednesday, July 30, 2014 11:55 AM > > > > To: bio-linux-announce at nebclists.nerc.ac.uk; Bio-Linux mailing list > > > > Subject: [Bio-linux-announce] Bio-Linux 8 now available > > > > > > > > Dear All, > > > > > > > > The Bio-Linux system gets a major new release every two years > > > > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS > > > > came out in April I've been working with help from the Bio-Linux > > > > community to make Bio-Linux 8 and it is now ready and available via > the new website. > > > > > > > > http://environmentalomics.org/bio-linux/ > > > > > > > > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I > > > > encourage you all to upgrade soon, as new bioinformatics packages > > > > will no longer be provided for Bio-Linux 7. See the "Installation" > > > > section for instructions on upgrading your BL7 machine. > > > > > > > > The new Ubuntu 14.04 base system brings many benefits such as > > > > increased hardware compatibility and new office and multimedia > > > > software, but Bio-Linux itself also has many improvements and > new/updated packages. > > > > Also for the first time there is a version in OVA format for > > > > VirtualBox/VMWare users, and this version will be updated whenever > > > > new ISO files are released. See the "What's New" and "Software List" > > > > pages on the website for details. > > > > > > > > As ever, please report problems and feedback to > > > > helpdesk at nebc.nerc.ac.uk. I can't promise to fix everything but > > > > will endeavour to provide help and squash bugs where I can. Also, > > > > please let me know if you use Bio-Linux for teaching or manage a > > > > large installation on your departmental server or computing lab. > > > > The more we can prove that people find this stuff useful, the more > likely we are to get future funding! > > > > > > > > I hope you enjoy using Bio-Linux 8. > > > > > > > > TIM > > > > > > > > -- > > > > Tim Booth > > > > NERC Environmental Bioinformatics Centre > > > > > > > > Centre for Ecology and Hydrology > > > > Maclean Bldg, Benson Lane > > > > Crowmarsh Gifford > > > > Wallingford, England > > > > OX10 8BB > > > > > > > > http://nebc.nerc.ac.uk > > > > +44 1491 69 2705 > > > > _______________________________________________ > > > > Bio-Linux-announce mailing list > > > > Bio-Linux-announce at nebclists.nerc.ac.uk > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce > > > > > > > > > > -- > > > Tim Booth > > > NERC Environmental Bioinformatics Centre > > > > > > Centre for Ecology and Hydrology > > > Maclean Bldg, Benson Lane > > > Crowmarsh Gifford > > > Wallingford, England > > > OX10 8BB > > > > > > http://nebc.nerc.ac.uk > > > +44 1491 69 2705 > > > > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > > > > > Stephen P. Molnar, Ph.D. Life is a > fuzzy set > > (614)312-7528 (c) > Stochastic and > multivariate > > Skype: smolnar1 > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Sun Aug 3 01:55:01 2014 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 3 Aug 2014 01:55:01 -0400 Subject: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now available In-Reply-To: References: <53dd34a0.a9bdb40a.081c.4fc7SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: Hi All I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/' followed by 'sudo ./install) but getting following error. I would really appreciate if somebody help me resolve this problem. Eventually I want to upgrade to Biolinux8. Thanks Tauqeer 2014-08-03T01:14:11-0400: execCmd: ./install --install [143] 2014-08-03T01:14:11-0400: Error: An error occurred when installing Parallels Tools. Please go to /var/log/parallels-tools-install.log for more information. 2014-08-03T01:14:15-0400: Exiting with code 1 2014-08-03T01:14:31-0400: Exiting with code 1 2014-08-03T01:30:07-0400: Parallels Tools 8.0.18619.1001606 Installer started. 2014-08-03T01:30:17-0400: execCmd: ./installer/pm.sh check_guest_tools 2>&1 [0] Sun Aug 3 01:30:17 EDT 2014 Start installation or upgrade of Guest Tools new version of parallels tools Installed Guest Tools were not found Perform installation into the /usr/lib/parallels-tools directory cat: /usr/lib/parallels-tools/kmods/../version: No such file or directory Start installation of prl_eth kernel module make: Entering directory `/usr/lib/parallels-tools/kmods' cd prl_eth/pvmnet && make make[1]: Entering directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' make -C /lib/modules/3.13.0-32-generic/build M=/usr/lib/parallels-tools/kmods/prl_eth/pvmnet make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' LD /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/built-in.o CC [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/pvmnet.o LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.o Building modules, stage 2. MODPOST 1 modules CC /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.mod.o LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.ko make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' make[1]: Leaving directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' cd prl_tg/Toolgate/Guest/Linux/prl_tg && make make[1]: Entering directory `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' make -C /lib/modules/3.13.0-32-generic/build SUBDIRS=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg SRCROOT=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg modules make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' CC [M] /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: In function ?prl_tg_write?: /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:9: error: implicit declaration of function ?PDE? [-Werror=implicit-function-declaration] /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:31: error: invalid type argument of ?->? (have ?int?) /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: In function ?prl_tg_init_one?: /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:2: error: implicit declaration of function ?create_proc_entry? [-Werror=implicit-function-declaration] /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:4: warning: assignment makes pointer from integer without a cast [enabled by default] /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1305:4: error: dereferencing pointer to incomplete type /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1306:4: error: dereferencing pointer to incomplete type cc1: some warnings being treated as errors make[3]: *** [/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o] Error 1 make[2]: *** [_module_/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg] Error 2 make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' make[1]: *** [prl_tg] Error 2 make[1]: Leaving directory `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' make: *** [installme] Error 2 make: Leaving directory `/usr/lib/parallels-tools/kmods' Error: could not build kernel modules Error: failed to install kernel modules On Sun, Aug 3, 2014 at 1:40 AM, Tauqeer Alam wrote: > Hi All > I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/' > followed by 'sudo ./install) but getting following error. I would really > appreciate if somebody help me resolve this problem. Eventually I want to > upgrade to Biolinux8. > > Thanks > > Tauqeer > > > On Sat, Aug 2, 2014 at 2:57 PM, Stephen P. Molnar > wrote: > >> Please see the following messages. >> >> >> >> Thanks in advance. >> >> >> >> Stephen P. Molnar, Ph.D. Life is a >> fuzzy set >> >> Foundation for Chemistry Stochastic and >> multivariate >> >> www.FoundationForChemistry.com >> >> (614)312-7528 (c) >> >> Skype: smolnar1 >> >> >> >> >> >> -----Original Message----- >> >> From: Tim Booth [mailto:tbooth at ceh.ac.uk ] >> >> Sent: Friday, August 01, 2014 9:40 AM >> >> To: Stephen P. Molnar >> >> Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available >> >> >> >> Hi Stephen, >> >> >> >> Glad you sorted out the shell. >> >> >> >> I'm sorry, but I can't say what might be up with the keyboard and I'm not >> going to start experimenting with XFCE right now as I have other >> priorities. You may well have more luck on the discussion mailing list: >> >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> >> >> >> Cheers, >> >> >> >> TIM >> >> >> >> On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote: >> >> > Thanks for the reply. As it turns out that was a red-faced forehead >> >> > slapping problem. After dispatching my note I realized that the shell >> >> > was zsh. >> >> > >> >> > Thanks to your reply I have successfully changed the default shell to >> >> > bash. >> >> > >> >> > There is, however anew problem, also a head scratcher for me. As I >> >> > don't like the Gnome shell and had become unenchanted with KDE, my >> >> > desktop of choice on my linux machines is XFCE, with Xfe as the file >> >> > manager of choice. I find that the keyboard doesn't seem to be >> >> > recognized by the xfwrite editor. On the other hand, nedit works as it >> >> > should. >> >> > >> >> > Your input about this problem would be much appreciated. >> >> > >> >> > Thanks in advance. >> >> > >> >> > Stephen P. Molnar, Ph.D. Life is a >> fuzzy set >> >> > Foundation for Chemistry Stochastic >> and multivariate >> >> > www.FoundationForChemistry.com >> >> > (614)312-7528 (c) >> >> > Skype: smolnar1 >> >> > >> >> > >> >> > -----Original Message----- >> >> > From: Tim Booth [mailto:tbooth at ceh.ac.uk ] >> >> > Sent: Friday, August 01, 2014 5:05 AM >> >> > To: Stephen P. Molnar >> >> > Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available >> >> > >> >> > Hi Stephen, >> >> > >> >> > Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so >> if you are a BASH fan you'll want to do: >> >> > >> >> > chsh -s /bin/bash >> >> > exec bash -l >> >> > >> >> > We do already have both L and ll aliased to that command, but not "l" >> >> > :-) >> >> > >> >> > Cheers, >> >> > >> >> > TIM >> >> > >> >> > On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote: >> >> > > I have encountered a rather strange problem with the new BioLinux v >> >> > > 8 latest. >> >> > > >> >> > > I installed the distribution in a VMware Player without any problems >> >> > > or error messages. In fact, I have a Debian v-7.6.0 distribution >> >> > > running in the same VMware device. Consequently, I have confidence >> >> > > in the virtual computer and my laptop on which it is running. >> >> > > >> >> > > I edited .bashrc to include the line alias l='ls -l --color' >> >> > > >> >> > > When I source the edited .bashrc file I get the following: >> >> > > >> >> > > computation at inga[computation] source >> .bashrc [ >> >> > > 2:57PM] >> >> > > .bashrc:16: command not found: shopt >> >> > > .bashrc:24: command not found: shopt >> >> > > .bashrc:108: command not found: shopt >> >> > > /usr/share/bash-completion/bash_completion:35: parse error near `]]' >> >> > > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ >> [ >> >> > > 2:57PM] >> >> > > >> >> > > The problem seems to be that shopt is missing! >> >> > > >> >> > > Please advise. >> >> > > >> >> > > Thanks in advance. >> >> > > >> >> > > Stephen P. Molnar, Ph.D. Life is a >> fuzzy >> >> > > set >> >> > > Foundation for Chemistry Stochastic >> and >> >> > > multivariate >> >> > > www.FoundationForChemistry.com >> >> > > (614)312-7528 (c) >> >> > > Skype: smolnar1 >> >> > > >> >> > > -----Original Message----- >> >> > > From: Tim Booth [mailto:tbooth at ceh.ac.uk ] >> >> > > Sent: Wednesday, July 30, 2014 11:55 AM >> >> > > To: bio-linux-announce at nebclists.nerc.ac.uk; Bio-Linux mailing list >> >> > > Subject: [Bio-linux-announce] Bio-Linux 8 now available >> >> > > >> >> > > Dear All, >> >> > > >> >> > > The Bio-Linux system gets a major new release every two years >> >> > > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS >> >> > > came out in April I've been working with help from the Bio-Linux >> >> > > community to make Bio-Linux 8 and it is now ready and available via >> the new website. >> >> > > >> >> > > http://environmentalomics.org/bio-linux/ >> >> > > >> >> > > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I >> >> > > encourage you all to upgrade soon, as new bioinformatics packages >> >> > > will no longer be provided for Bio-Linux 7. See the "Installation" >> >> > > section for instructions on upgrading your BL7 machine. >> >> > > >> >> > > The new Ubuntu 14.04 base system brings many benefits such as >> >> > > increased hardware compatibility and new office and multimedia >> >> > > software, but Bio-Linux itself also has many improvements and >> new/updated packages. >> >> > > Also for the first time there is a version in OVA format for >> >> > > VirtualBox/VMWare users, and this version will be updated whenever >> >> > > new ISO files are released. See the "What's New" and "Software List" >> >> > > pages on the website for details. >> >> > > >> >> > > As ever, please report problems and feedback to >> >> > > helpdesk at nebc.nerc.ac.uk. I can't promise to fix everything but >> >> > > will endeavour to provide help and squash bugs where I can. Also, >> >> > > please let me know if you use Bio-Linux for teaching or manage a >> >> > > large installation on your departmental server or computing lab. >> >> > > The more we can prove that people find this stuff useful, the more >> likely we are to get future funding! >> >> > > >> >> > > I hope you enjoy using Bio-Linux 8. >> >> > > >> >> > > TIM >> >> > > >> >> > > -- >> >> > > Tim Booth >> >> > > NERC Environmental Bioinformatics Centre >> >> > > >> >> > > Centre for Ecology and Hydrology >> >> > > Maclean Bldg, Benson Lane >> >> > > Crowmarsh Gifford >> >> > > Wallingford, England >> >> > > OX10 8BB >> >> > > >> >> > > http://nebc.nerc.ac.uk >> >> > > +44 1491 69 2705 >> >> > > _______________________________________________ >> >> > > Bio-Linux-announce mailing list >> >> > > Bio-Linux-announce at nebclists.nerc.ac.uk >> >> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce >> >> > > >> >> > >> >> > -- >> >> > Tim Booth >> >> > NERC Environmental Bioinformatics Centre >> >> > >> >> > Centre for Ecology and Hydrology >> >> > Maclean Bldg, Benson Lane >> >> > Crowmarsh Gifford >> >> > Wallingford, England >> >> > OX10 8BB >> >> > >> >> > http://nebc.nerc.ac.uk >> >> > +44 1491 69 2705 >> >> > >> >> >> >> -- >> >> Tim Booth >> >> NERC Environmental Bioinformatics Centre >> >> >> >> Centre for Ecology and Hydrology >> >> Maclean Bldg, Benson Lane >> >> Crowmarsh Gifford >> >> Wallingford, England >> >> OX10 8BB >> >> >> >> http://nebc.nerc.ac.uk >> >> +44 1491 69 2705 >> >> >> >> >> >> Stephen P. Molnar, Ph.D. Life is a >> fuzzy set >> >> (614)312-7528 (c) >> Stochastic and >> multivariate >> >> Skype: smolnar1 >> >> >> >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> >> > > > -- > ********************************************* > Md Tauqeer Alam, Ph.D > Division of Infectious Diseases > Emory University School of Medicine > 615 Michael Street, Atlanta, GA 30322, USA > tauqeer9 at gmail.com > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Sun Aug 3 04:54:07 2014 From: gawbul at gmail.com (Steve Moss) Date: Sun, 3 Aug 2014 09:54:07 +0100 Subject: [Bio-Linux] Parallels Message-ID: Dear Tauqeer, Could you post your /var/log/parallels-tools-install.log on pastebin.com and share a link to it please? What system are you running on? BioLinux 7/Ubuntu 12.04? What version of Parallels are you using? I found some posts referring to problems with Ubuntu/kernel support in various versions of Parallels. It seems they take a while to include support for more recent kernels and/or Ubuntu releases. Try the following in the first instance to ensure your build environment is configured correctly: sudo apt-get install build-essential linux-headers-$(uname -r) Cheers, Steve On 3 August 2014 06:55, wrote: > Message: 2 > Date: Sun, 3 Aug 2014 01:55:01 -0400 > From: Tauqeer Alam > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now > available > Message-ID: > < > CAFaE85Bg059MDyX5285LLXj8qhei8M1oBHAtXJBCsZdRvEmE0w at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi All > I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/' > followed by 'sudo ./install) but getting following error. I would really > appreciate if somebody help me resolve this problem. Eventually I want to > upgrade to Biolinux8. > > Thanks > > Tauqeer > > 2014-08-03T01:14:11-0400: execCmd: ./install --install [143] > 2014-08-03T01:14:11-0400: Error: An error occurred when installing > Parallels Tools. Please go to /var/log/parallels-tools-install.log for more > information. > 2014-08-03T01:14:15-0400: Exiting with code 1 > 2014-08-03T01:14:31-0400: Exiting with code 1 > 2014-08-03T01:30:07-0400: > > Parallels Tools 8.0.18619.1001606 Installer started. > 2014-08-03T01:30:17-0400: execCmd: ./installer/pm.sh check_guest_tools 2>&1 > [0] > > Sun Aug 3 01:30:17 EDT 2014 > Start installation or upgrade of Guest Tools > new version of parallels tools > Installed Guest Tools were not found > Perform installation into the /usr/lib/parallels-tools directory > cat: /usr/lib/parallels-tools/kmods/../version: No such file or directory > Start installation of prl_eth kernel module > make: Entering directory `/usr/lib/parallels-tools/kmods' > cd prl_eth/pvmnet && make > make[1]: Entering directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' > make -C /lib/modules/3.13.0-32-generic/build > M=/usr/lib/parallels-tools/kmods/prl_eth/pvmnet > make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' > LD /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/built-in.o > CC [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/pvmnet.o > LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.o > Building modules, stage 2. > MODPOST 1 modules > CC /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.mod.o > LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.ko > make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' > make[1]: Leaving directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' > cd prl_tg/Toolgate/Guest/Linux/prl_tg && make > make[1]: Entering directory > `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' > make -C /lib/modules/3.13.0-32-generic/build > SUBDIRS=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg > SRCROOT=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg > modules > make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' > CC [M] > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: > In function ?prl_tg_write?: > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:9: > error: implicit declaration of function ?PDE? > [-Werror=implicit-function-declaration] > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:31: > error: invalid type argument of ?->? (have ?int?) > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: > In function ?prl_tg_init_one?: > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:2: > error: implicit declaration of function ?create_proc_entry? > [-Werror=implicit-function-declaration] > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:4: > warning: assignment makes pointer from integer without a cast [enabled by > default] > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1305:4: > error: dereferencing pointer to incomplete type > > /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1306:4: > error: dereferencing pointer to incomplete type > cc1: some warnings being treated as errors > make[3]: *** > [/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o] > Error 1 > make[2]: *** > [_module_/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg] > Error 2 > make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' > make[1]: *** [prl_tg] Error 2 > make[1]: Leaving directory > `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' > make: *** [installme] Error 2 > make: Leaving directory `/usr/lib/parallels-tools/kmods' > Error: could not build kernel modules > Error: failed to install kernel modules > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Sun Aug 3 08:16:49 2014 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 3 Aug 2014 08:16:49 -0400 Subject: [Bio-Linux] Parallels In-Reply-To: References: Message-ID: Thanks Steve. The screen output for "sudo apt-get install build-essential linux-headers-$(uname -r)" command is- Reading package lists... Done Building dependency tree Reading state information... Done build-essential is already the newest version. linux-headers-3.13.0-32-generic is already the newest version. The following packages were automatically installed and are no longer required: bluez-alsa:i386 natefoo-taxonomy libhal-storage1 python-numexpr libgudev-1.0-0:i386 libcairo-gobject2:i386 libavc1394-0:i386 linux-headers-3.2.0-48 libproxy1:i386 firefox-globalmenu libspeex1:i386 python-gnuplot libwavpack1:i386 libsoup-gnome2.4-1:i386 gstreamer0.10-plugins-good:i386 libiec61883-0:i386 libhal1 hal linux-headers-3.2.0-48-generic libaa1:i386 libhdf5-serial-1.8.4 liblzo2-2 language-pack-kde-en libraw1394-11:i386 libshout3:i386 libdv4:i386 gstreamer0.10-x:i386 natefoo-add-scores libgnome-keyring0:i386 galaxy-server-test python-tables libtag1c2a:i386 master-pdf-editor-bin:i386 hal-info macs14 libkms1 language-pack-kde-en-base libxv1:i386 glib-networking:i386 libsoup2.4-1:i386 libtag1-vanilla:i386 Use 'apt-get autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. Here is the link for /var/log/parallels-tools- install.log- http://pastebin.com/qBT8ZvQR I am using Biolinux7, Ubuntu 12.04 LTS and the parallel is Parallels Desktop 8 for Mac Build 8.0.18619 Thanks for your help. Tauqeer On Sun, Aug 3, 2014 at 4:54 AM, Steve Moss wrote: > Dear Tauqeer, > > Could you post your /var/log/parallels-tools-install.log on pastebin.com > and share a link to it please? What system are you running on? BioLinux > 7/Ubuntu 12.04? What version of Parallels are you using? I found some posts > referring to problems with Ubuntu/kernel support in various versions of > Parallels. It seems they take a while to include support for more recent > kernels and/or Ubuntu releases. > > Try the following in the first instance to ensure your build environment > is configured correctly: > > sudo apt-get install build-essential linux-headers-$(uname -r) > > Cheers, > > Steve > > On 3 August 2014 06:55, wrote: > >> Message: 2 >> Date: Sun, 3 Aug 2014 01:55:01 -0400 >> From: Tauqeer Alam >> To: Bio-Linux help and discussion >> Subject: Re: [Bio-Linux] FW: [Bio-linux-announce] Bio-Linux 8 now >> available >> Message-ID: >> < >> CAFaE85Bg059MDyX5285LLXj8qhei8M1oBHAtXJBCsZdRvEmE0w at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi All >> I am trying to reinstall Parallels Tools ('cd /media/Parallels\ Tools/' >> followed by 'sudo ./install) but getting following error. I would really >> appreciate if somebody help me resolve this problem. Eventually I want to >> upgrade to Biolinux8. >> >> Thanks >> >> Tauqeer >> >> 2014-08-03T01:14:11-0400: execCmd: ./install --install [143] >> 2014-08-03T01:14:11-0400: Error: An error occurred when installing >> Parallels Tools. Please go to /var/log/parallels-tools-install.log for >> more >> information. >> 2014-08-03T01:14:15-0400: Exiting with code 1 >> 2014-08-03T01:14:31-0400: Exiting with code 1 >> 2014-08-03T01:30:07-0400: >> >> Parallels Tools 8.0.18619.1001606 Installer started. >> 2014-08-03T01:30:17-0400: execCmd: ./installer/pm.sh check_guest_tools >> 2>&1 >> [0] >> >> Sun Aug 3 01:30:17 EDT 2014 >> Start installation or upgrade of Guest Tools >> new version of parallels tools >> Installed Guest Tools were not found >> Perform installation into the /usr/lib/parallels-tools directory >> cat: /usr/lib/parallels-tools/kmods/../version: No such file or directory >> Start installation of prl_eth kernel module >> make: Entering directory `/usr/lib/parallels-tools/kmods' >> cd prl_eth/pvmnet && make >> make[1]: Entering directory >> `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' >> make -C /lib/modules/3.13.0-32-generic/build >> M=/usr/lib/parallels-tools/kmods/prl_eth/pvmnet >> make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' >> LD /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/built-in.o >> CC [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/pvmnet.o >> LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.o >> Building modules, stage 2. >> MODPOST 1 modules >> CC /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.mod.o >> LD [M] /usr/lib/parallels-tools/kmods/prl_eth/pvmnet/prl_eth.ko >> make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' >> make[1]: Leaving directory `/usr/lib/parallels-tools/kmods/prl_eth/pvmnet' >> cd prl_tg/Toolgate/Guest/Linux/prl_tg && make >> make[1]: Entering directory >> `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' >> make -C /lib/modules/3.13.0-32-generic/build >> SUBDIRS=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg >> SRCROOT=/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg >> modules >> make[2]: Entering directory `/usr/src/linux-headers-3.13.0-32-generic' >> CC [M] >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: >> In function ?prl_tg_write?: >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:9: >> error: implicit declaration of function ?PDE? >> [-Werror=implicit-function-declaration] >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:796:31: >> error: invalid type argument of ?->? (have ?int?) >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c: >> In function ?prl_tg_init_one?: >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:2: >> error: implicit declaration of function ?create_proc_entry? >> [-Werror=implicit-function-declaration] >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1303:4: >> warning: assignment makes pointer from integer without a cast [enabled by >> default] >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1305:4: >> error: dereferencing pointer to incomplete type >> >> /usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.c:1306:4: >> error: dereferencing pointer to incomplete type >> cc1: some warnings being treated as errors >> make[3]: *** >> >> [/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg/prltg.o] >> Error 1 >> make[2]: *** >> >> [_module_/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg] >> Error 2 >> make[2]: Leaving directory `/usr/src/linux-headers-3.13.0-32-generic' >> make[1]: *** [prl_tg] Error 2 >> make[1]: Leaving directory >> `/usr/lib/parallels-tools/kmods/prl_tg/Toolgate/Guest/Linux/prl_tg' >> make: *** [installme] Error 2 >> make: Leaving directory `/usr/lib/parallels-tools/kmods' >> Error: could not build kernel modules >> Error: failed to install kernel modules >> > > > -- > > Steve Moss > about.me/gawbul > [image: Steve Moss on about.me] > > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Sun Aug 3 09:46:57 2014 From: gawbul at gmail.com (Steve Moss) Date: Sun, 3 Aug 2014 14:46:57 +0100 Subject: [Bio-Linux] Parallels Message-ID: Dear Tauqeer, Great, thanks! The build environment seems to be setup okay. The problem seems to be a lack of support for Ubuntu 12.04 in Parallels Desktop 8. See here http://kb.parallels.com/en/122353. It recommends upgrading to Parallels Desktop 9. I'd just go with VirtualBox to be honest. Though there is also VMWare Fusion if you don't want the full VM overheads. Cheers, Steve On 3 August 2014 13:16, Tauqeer Alam wrote: > Thanks Steve. The screen output for "sudo apt-get install build-essential > linux-headers-$(uname -r)" command is- > > Reading package lists... Done > Building dependency tree > Reading state information... Done > build-essential is already the newest version. > linux-headers-3.13.0-32-generic is already the newest version. > The following packages were automatically installed and are no longer > required: > bluez-alsa:i386 natefoo-taxonomy libhal-storage1 python-numexpr > libgudev-1.0-0:i386 libcairo-gobject2:i386 > libavc1394-0:i386 linux-headers-3.2.0-48 libproxy1:i386 > firefox-globalmenu libspeex1:i386 python-gnuplot > libwavpack1:i386 libsoup-gnome2.4-1:i386 gstreamer0.10-plugins-good:i386 > libiec61883-0:i386 libhal1 hal > linux-headers-3.2.0-48-generic libaa1:i386 libhdf5-serial-1.8.4 > liblzo2-2 language-pack-kde-en > libraw1394-11:i386 libshout3:i386 libdv4:i386 gstreamer0.10-x:i386 > natefoo-add-scores libgnome-keyring0:i386 > galaxy-server-test python-tables libtag1c2a:i386 > master-pdf-editor-bin:i386 hal-info macs14 libkms1 > language-pack-kde-en-base libxv1:i386 glib-networking:i386 > libsoup2.4-1:i386 libtag1-vanilla:i386 > Use 'apt-get autoremove' to remove them. > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > > Here is the link for /var/log/parallels-tools- > install.log- > http://pastebin.com/qBT8ZvQR > > I am using Biolinux7, Ubuntu 12.04 LTS and the parallel is Parallels > Desktop 8 for Mac Build 8.0.18619 > > Thanks for your help. > > Tauqeer > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Sun Aug 3 11:19:09 2014 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 3 Aug 2014 11:19:09 -0400 Subject: [Bio-Linux] Parallels In-Reply-To: References: Message-ID: Thank you very much Steve. I just upgraded to Parallels Desktop 9, and it worked. Everything is perfectly alright now. Thanks again for taking time to help me. Tauqeer On Sun, Aug 3, 2014 at 9:46 AM, Steve Moss wrote: > Dear Tauqeer, > > Great, thanks! The build environment seems to be setup okay. > > The problem seems to be a lack of support for Ubuntu 12.04 in Parallels > Desktop 8. See here http://kb.parallels.com/en/122353. It recommends > upgrading to Parallels Desktop 9. I'd just go with VirtualBox to be honest. > Though there is also VMWare Fusion if you don't want the full VM overheads. > > Cheers, > > Steve > > On 3 August 2014 13:16, Tauqeer Alam wrote: > >> Thanks Steve. The screen output for "sudo apt-get install build-essential >> linux-headers-$(uname -r)" command is- >> >> Reading package lists... Done >> Building dependency tree >> Reading state information... Done >> build-essential is already the newest version. >> linux-headers-3.13.0-32-generic is already the newest version. >> The following packages were automatically installed and are no longer >> required: >> bluez-alsa:i386 natefoo-taxonomy libhal-storage1 python-numexpr >> libgudev-1.0-0:i386 libcairo-gobject2:i386 >> libavc1394-0:i386 linux-headers-3.2.0-48 libproxy1:i386 >> firefox-globalmenu libspeex1:i386 python-gnuplot >> libwavpack1:i386 libsoup-gnome2.4-1:i386 >> gstreamer0.10-plugins-good:i386 libiec61883-0:i386 libhal1 hal >> linux-headers-3.2.0-48-generic libaa1:i386 libhdf5-serial-1.8.4 >> liblzo2-2 language-pack-kde-en >> libraw1394-11:i386 libshout3:i386 libdv4:i386 gstreamer0.10-x:i386 >> natefoo-add-scores libgnome-keyring0:i386 >> galaxy-server-test python-tables libtag1c2a:i386 >> master-pdf-editor-bin:i386 hal-info macs14 libkms1 >> language-pack-kde-en-base libxv1:i386 glib-networking:i386 >> libsoup2.4-1:i386 libtag1-vanilla:i386 >> Use 'apt-get autoremove' to remove them. >> 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. >> >> Here is the link for /var/log/parallels-tools- >> install.log- >> http://pastebin.com/qBT8ZvQR >> >> I am using Biolinux7, Ubuntu 12.04 LTS and the parallel is Parallels >> Desktop 8 for Mac Build 8.0.18619 >> >> Thanks for your help. >> >> Tauqeer >> > > -- > > Steve Moss > about.me/gawbul > [image: Steve Moss on about.me] > > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From rjrich at umich.edu Sun Aug 3 11:31:10 2014 From: rjrich at umich.edu (Rudy J. Richardson) Date: Sun, 3 Aug 2014 11:31:10 -0400 (EDT) Subject: [Bio-Linux] Parallels In-Reply-To: References: Message-ID: Hi, fyi, I have compared Parallels 9, VMware Fusion 6, and VB 4.3.14 on my MacPro 6.1 under OS X 10.9.4. Each virtualization program works, but for good graphics performance, Parallels 9 is far superior to the other two. The graphics performance of VB is the poorest by far. I have tested this with linux (Ubuntu 12.04, 12.1, 14.04, Mint 13, 17, and Windows 7 guests. Regarding DEs for linux, I get the best results with Xfce. KDE also works, and I have found instabilities in Cinnamon and MATE. rjrich On Sun, 3 Aug 2014, Tauqeer Alam wrote: > Thank you very much Steve. I just upgraded to Parallels Desktop 9, and it > worked. Everything is perfectly alright now. Thanks again for taking time to > help me. > > Tauqeer > > > On Sun, Aug 3, 2014 at 9:46 AM, Steve Moss wrote: > Dear Tauqeer, > Great, thanks! The build environment seems to be setup okay. > > The problem seems to be a lack of support for Ubuntu 12.04 in > Parallels Desktop 8. See here?http://kb.parallels.com/en/122353. It > recommends upgrading to Parallels Desktop 9. I'd just go with > VirtualBox to be honest. Though there is also VMWare Fusion if you > don't want the full VM overheads. > > Cheers, > > Steve > > On 3 August 2014 13:16, Tauqeer Alam wrote: > Thanks Steve. The screen output for "sudo apt-get install > build-essential linux-headers-$(uname -r)" command is- > > Reading package lists... Done > Building dependency tree?????? > Reading state information... Done > build-essential is already the newest version. > linux-headers-3.13.0-32-generic is already the newest > version. > The following packages were automatically installed and > are no longer required: > ? bluez-alsa:i386 natefoo-taxonomy libhal-storage1 > python-numexpr libgudev-1.0-0:i386 libcairo-gobject2:i386 > ? libavc1394-0:i386 linux-headers-3.2.0-48 libproxy1:i386 > firefox-globalmenu libspeex1:i386 python-gnuplot > ? libwavpack1:i386 libsoup-gnome2.4-1:i386 > gstreamer0.10-plugins-good:i386 libiec61883-0:i386 libhal1 > hal > ? linux-headers-3.2.0-48-generic libaa1:i386 > libhdf5-serial-1.8.4 liblzo2-2 language-pack-kde-en > ? libraw1394-11:i386 libshout3:i386 libdv4:i386 > gstreamer0.10-x:i386 natefoo-add-scores > libgnome-keyring0:i386 > ? galaxy-server-test python-tables libtag1c2a:i386 > master-pdf-editor-bin:i386 hal-info macs14 libkms1 > ? language-pack-kde-en-base libxv1:i386 > glib-networking:i386 libsoup2.4-1:i386 > libtag1-vanilla:i386 > Use 'apt-get autoremove' to remove them. > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to > upgrade. > > Here is the link for? /var/log/parallels-tools-install.log- > http://pastebin.com/qBT8ZvQR > > I am using Biolinux7, Ubuntu 12.04 LTS and the parallel is > Parallels Desktop 8 for Mac Build 8.0.18619 > > Thanks for your help. > > Tauqeer > > > -- > ? > Steve Moss > about.me/gawbul > Steve Moss on about.me > ? > > > > > -- > ********************************************* > Md Tauqeer Alam, Ph.D > Division of Infectious Diseases > Emory University School of Medicine > 615 Michael Street,?Atlanta, GA 30322, USA > tauqeer9 at gmail.com > > From gawbul at gmail.com Sun Aug 3 12:42:47 2014 From: gawbul at gmail.com (Steve Moss) Date: Sun, 3 Aug 2014 17:42:47 +0100 Subject: [Bio-Linux] Graphics Performance in VMs Message-ID: Dear Rudy, Parallels and Fusion are slightly different to VirtualBox as they can be considered similar to container-based or OS-level virtualisation, rather than full-blown hypervisor-based virtualisation. With regards to VirtualBox graphics performance. Did you install the Guest Additions in the guest OS, as well as increasing available video memory and enabling acceleration in the VM settings? I find that these improve things greatly. I certainly agree re Xfce. Hence why Xubuntu is so great for lower end machines/laptops. Cheers, Steve On 3 August 2014 16:31, Rudy J. Richardson wrote: > Hi, > > fyi, I have compared Parallels 9, VMware Fusion 6, and VB 4.3.14 on my > MacPro 6.1 under OS X 10.9.4. > > Each virtualization program works, but for good graphics performance, > Parallels 9 is far superior to the other two. The graphics performance of > VB is the poorest by far. I have tested this with linux (Ubuntu 12.04, > 12.1, 14.04, Mint 13, 17, and Windows 7 guests. > > Regarding DEs for linux, I get the best results with Xfce. KDE also works, > and I have found instabilities in Cinnamon and MATE. > > rjrich -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From rjrich at umich.edu Sun Aug 3 12:58:22 2014 From: rjrich at umich.edu (Rudy J. Richardson) Date: Sun, 3 Aug 2014 12:58:22 -0400 (EDT) Subject: [Bio-Linux] Graphics Performance in VMs In-Reply-To: References: Message-ID: Yes, I maxed out the video settings on VB as well as on Parallels and VMware Fusion. I also installed the additional tools in each case. One way that I assess relative video performance is to run a graphics-intensive molcular modeling program, YASARA. With Parallels, YASARA runs passbly well, whereas under VB, I get a flickering screen with YASARA and cannot really run the program. VMware Fusion is intermediate between Parallels and VB. Regarding Xfce, I have found that the Mint implementation of Xfce is particularly nice. It looks superb right out of the box with Mint's default settings. On Sun, 3 Aug 2014, Steve Moss wrote: > Dear Rudy, > Parallels and Fusion are slightly different to VirtualBox as they can be > considered similar to container-based or OS-level virtualisation, rather > than full-blown hypervisor-based virtualisation. > > With regards to VirtualBox graphics performance. Did you install the Guest > Additions in the guest OS, as well as increasing available video memory and > enabling acceleration in the VM settings? I find that these improve things > greatly. > > I certainly agree re Xfce. Hence why Xubuntu is so great for lower end > machines/laptops. > > Cheers, > > Steve > > On 3 August 2014 16:31, Rudy J. Richardson wrote: > Hi, > > fyi, I have compared Parallels 9, VMware Fusion 6, and VB 4.3.14 > on my MacPro 6.1 under OS X 10.9.4. > > Each virtualization program works, but for good graphics > performance, Parallels 9 is far superior to the other two. The > graphics performance of VB is the poorest by far. I have tested > this with linux (Ubuntu 12.04, 12.1, 14.04, Mint 13, 17, and > Windows 7 guests. > > Regarding DEs for linux, I get the best results with Xfce. KDE > also works, and I have found instabilities in Cinnamon and MATE. > > rjrich > > > -- > ? > Steve Moss > about.me/gawbul > Steve Moss on about.me > ? > > From tbooth at ceh.ac.uk Mon Aug 4 09:30:42 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Aug 2014 14:30:42 +0100 Subject: [Bio-Linux] Parallels In-Reply-To: References: Message-ID: <1407159042.6360.61.camel@balisaur> Hi Rudy, Thanks for sharing your experience of Parallels, VB, etc. It's interesting to hear that Parallels 9 makes such a difference to graphics performance. If you do get around to trying the OVA version of Bio-Linux 8 on Parallels I'd be interested to hear if it works and if there are any tips/tweaks that Parallels users could benefit from that I could put up on the website. I've now tested the OVA on VMWare Workstation 10 and it throws a couple of warnings but then seems to work fine. You may have noticed that MATE is the new default 2D desktop in BL8, as I wanted some continuity from "Gnome classic". I've been using it for the last few weeks and found it pretty stable, but maybe I've not stressed it enough, or else the newer version addresses the issues, or else they only appear on Parallels. All feedback and observations in this area are gratefully received. Cheers, TIM On Sun, 2014-08-03 at 16:31 +0100, Rudy J. Richardson wrote: > Hi, > > fyi, I have compared Parallels 9, VMware Fusion 6, and VB 4.3.14 on my > MacPro 6.1 under OS X 10.9.4. > > Each virtualization program works, but for good graphics performance, > Parallels 9 is far superior to the other two. The graphics performance of > VB is the poorest by far. I have tested this with linux (Ubuntu 12.04, > 12.1, 14.04, Mint 13, 17, and Windows 7 > guests. > > Regarding DEs for linux, I get the best results with Xfce. KDE also works, > and I have found instabilities in Cinnamon and MATE. > > rjrich > From tbooth at ceh.ac.uk Tue Aug 5 14:21:46 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 5 Aug 2014 19:21:46 +0100 Subject: [Bio-Linux] Bio-Linux 8 small fixes Message-ID: <1407262906.6360.225.camel@balisaur> Dear Bio-Linux users, Since the release of Bio-Linux 8 I've had a few people reporting minor glitches with the system, which I've been working to address, but generally feedback has been good. :-) This is to let you know that I just put up a new ISO (and matching OVA) today that incorporates various small fixes, and most significantly restores the bioinformatics Dash menu so that you can more conveniently access all the tools (or at least the GUI tools) on the system. See this if you're not sure what I mean: http://nebc.nerc.ac.uk/downloads/bl8_only/biomenu.png If you are already running BL8, to be sure you get the fixes you should run the upgrade script again (this also applies if you installed BL8 directly) : sudo apt-get install runurl sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh (and reboot) The script is designed to only install stuff it sees is missing, so if the system is already up-to-date it should finish in around a minute and then report "All done - your system is updated to Bio-Linux 8". Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From gawbul at gmail.com Wed Aug 6 07:50:02 2014 From: gawbul at gmail.com (Steve Moss) Date: Wed, 6 Aug 2014 12:50:02 +0100 Subject: [Bio-Linux] Bio-Linux 8 small fixes (Tim Booth) Message-ID: Dear Tim, This probably won't affect most, but I use MariaDB rather than MySQL, which caused errors with the update. I needed to extract the files from upgrade8.sh using sharutils and edit the bl_master_package_list.txt to replace mysql-client etc. with mariadb-client etc.. I'd personally recommend everyone use MariaDB (a fork and drop in replacement of MySQL developed by SkySQL), with the plans that the evil Oracle no doubt have for MySQL in the long run. Cheers, Steve On 6 August 2014 12:00, wrote: > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-Linux digest..." > > > Today's Topics: > > 1. Bio-Linux 8 small fixes (Tim Booth) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Aug 2014 19:21:46 +0100 > From: Tim Booth > To: Bio-Linux mailing list > Subject: [Bio-Linux] Bio-Linux 8 small fixes > Message-ID: <1407262906.6360.225.camel at balisaur> > Content-Type: text/plain; charset="UTF-8" > > Dear Bio-Linux users, > > Since the release of Bio-Linux 8 I've had a few people reporting minor > glitches with the system, which I've been working to address, but > generally feedback has been good. :-) > > This is to let you know that I just put up a new ISO (and matching OVA) > today that incorporates various small fixes, and most significantly > restores the bioinformatics Dash menu so that you can more conveniently > access all the tools (or at least the GUI tools) on the system. > > See this if you're not sure what I mean: > http://nebc.nerc.ac.uk/downloads/bl8_only/biomenu.png > > If you are already running BL8, to be sure you get the fixes you should > run the upgrade script again (this also applies if you installed BL8 > directly) : > > sudo apt-get install runurl > sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > (and reboot) > > The script is designed to only install stuff it sees is missing, so if > the system is already up-to-date it should finish in around a minute and > then report "All done - your system is updated to Bio-Linux 8". > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > ------------------------------ > > End of Bio-Linux Digest, Vol 71, Issue 9 > **************************************** > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Aug 6 09:07:01 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 6 Aug 2014 14:07:01 +0100 Subject: [Bio-Linux] Bio-Linux 8 small fixes (Tim Booth) In-Reply-To: References: Message-ID: <1407330421.6360.278.camel@balisaur> Hi Steve, I never really thought about this as I always use PostgreSQL wherever I can. We used to ship some tools that needed MySQL installed but given they are pretty much obsolete I might just take MySQL off the image entirely and people can "apt-get install" what they actually want. By the way, if anyone else needs to tinker with the script in a similar way, just set UNPACK_ONLY before you run it - eg. $ env UNPACK_ONLY=1 runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh The script will say: ... Unpack complete in /tmp/tmp.3NynzJEmL8. Exiting. Then: $ mv /tmp/tmp.3NynzJEmL8 ./upgrader_unpacked $ cd ./upgrader_unpacked $ sudo bash ./upgrade_to_8.sh Cheers, TIM > This probably won't affect most, but I use MariaDB rather than MySQL, > which caused errors with the update. I needed to extract the files > from upgrade8.sh using sharutils and edit the > bl_master_package_list.txt to replace mysql-client etc. with > mariadb-client etc.. > > I'd personally recommend everyone use MariaDB (a fork and drop in > replacement of MySQL developed by SkySQL), with the plans that the > evil Oracle no doubt have for MySQL in the long run. > > Cheers, > > Steve > > > On 6 August 2014 12:00, > wrote: > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Bio-Linux digest..." > > > Today's Topics: > > 1. Bio-Linux 8 small fixes (Tim Booth) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Aug 2014 19:21:46 +0100 > From: Tim Booth > To: Bio-Linux mailing list > Subject: [Bio-Linux] Bio-Linux 8 small fixes > Message-ID: <1407262906.6360.225.camel at balisaur> > Content-Type: text/plain; charset="UTF-8" > > Dear Bio-Linux users, > > Since the release of Bio-Linux 8 I've had a few people > reporting minor > glitches with the system, which I've been working to address, > but > generally feedback has been good. :-) > > This is to let you know that I just put up a new ISO (and > matching OVA) > today that incorporates various small fixes, and most > significantly > restores the bioinformatics Dash menu so that you can more > conveniently > access all the tools (or at least the GUI tools) on the > system. > > See this if you're not sure what I mean: > http://nebc.nerc.ac.uk/downloads/bl8_only/biomenu.png > > If you are already running BL8, to be sure you get the fixes > you should > run the upgrade script again (this also applies if you > installed BL8 > directly) : > > sudo apt-get install runurl > sudo runurl > http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > (and reboot) > > The script is designed to only install stuff it sees is > missing, so if > the system is already up-to-date it should finish in around a > minute and > then report "All done - your system is updated to Bio-Linux > 8". > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > ------------------------------ > > End of Bio-Linux Digest, Vol 71, Issue 9 > **************************************** > > > > -- > > Steve Moss > about.me/gawbul > Steve Moss on about.me > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From andreas.leimbach at uni-wuerzburg.de Wed Aug 6 16:10:10 2014 From: andreas.leimbach at uni-wuerzburg.de (Andreas Leimbach) Date: Wed, 06 Aug 2014 22:10:10 +0200 Subject: [Bio-Linux] newest sequin version In-Reply-To: <1407330421.6360.278.camel@balisaur> References: <1407330421.6360.278.camel@balisaur> Message-ID: <53E28BA2.206@uni-wuerzburg.de> Hi Tim and BL community, first of all, awesome BL8 release. Runs like a charm on our machines, dash bioinfo lens and all, thanks a lot. NCBIs sequin is preinstalled in the distro, however I wanted to run a newer version. I got the new 64 bit version from NCBIs ftp server: $ wget ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz But, it always quits with an error that some library can't be found: $ ./sequin ./sequin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Do you guys have an idea how to solve this? I already tried to install the old ia32-libs with a work-around, they got disconnected in 13.10 I think (I also tried the 32 bit sequin version, misses 'libXm.so.4'). Thanks. Best, Andreas -- Andreas Leimbach Universit?t M?nster Institut f?r Hygiene Mendelstr. 7 D-48149 M?nster Germany Tel.: +49 (0)551 39 33843 E-Mail: andreas.leimbach at uni-wuerzburg.de From gawbul at gmail.com Thu Aug 7 09:08:35 2014 From: gawbul at gmail.com (Steve Moss) Date: Thu, 7 Aug 2014 14:08:35 +0100 Subject: [Bio-Linux] newest sequin version Message-ID: Dear Andreas, You need to install libjpeg62 (hence the libjpeg.so.62 in the error message), perhaps libjpeg62-dev too?: sudo apt-get install libjpeg62 libjpeg62-dev Cheers, Steve On 7 August 2014 12:00, wrote: > Date: Wed, 06 Aug 2014 22:10:10 +0200 > From: Andreas Leimbach > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] newest sequin version > Message-ID: <53E28BA2.206 at uni-wuerzburg.de> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi Tim and BL community, > > first of all, awesome BL8 release. Runs like a charm on our machines, > dash bioinfo lens and all, thanks a lot. > NCBIs sequin is preinstalled in the distro, however I wanted to run a > newer version. I got the new 64 bit version from NCBIs ftp server: > > $ wget ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz > > But, it always quits with an error that some library can't be found: > > $ ./sequin > ./sequin: error while loading shared libraries: libjpeg.so.62: cannot > open shared object file: No such file or directory > > Do you guys have an idea how to solve this? I already tried to install > the old ia32-libs with a work-around, they got disconnected in 13.10 I > think (I also tried the 32 bit sequin version, misses 'libXm.so.4'). > Thanks. > > Best, > Andreas > > > -- > Andreas Leimbach > Universit?t M?nster > Institut f?r Hygiene > Mendelstr. 7 > D-48149 M?nster > Germany > > Tel.: +49 (0)551 39 33843 > E-Mail: andreas.leimbach at uni-wuerzburg.de > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas.leimbach at uni-wuerzburg.de Thu Aug 7 09:22:48 2014 From: andreas.leimbach at uni-wuerzburg.de (Andreas Leimbach) Date: Thu, 07 Aug 2014 15:22:48 +0200 Subject: [Bio-Linux] newest sequin version In-Reply-To: References: Message-ID: <53E37DA8.2000706@uni-wuerzburg.de> Hey Steve, that was it, doh. Thanks a lot! Cheers, Andreas -- Andreas Leimbach Universit?t M?nster Institut f?r Hygiene Mendelstr. 7 D-48149 M?nster Germany Tel.: +49 (0)551 39 33843 E-Mail: andreas.leimbach at uni-wuerzburg.de On 07.08.2014 15:08, Steve Moss wrote: > Dear Andreas, > > You need to install libjpeg62 (hence the libjpeg.so.62 in the error > message), perhaps libjpeg62-dev too?: > > sudo apt-get install libjpeg62 libjpeg62-dev > > Cheers, > > Steve > > On 7 August 2014 12:00, wrote: > >> Date: Wed, 06 Aug 2014 22:10:10 +0200 >> From: Andreas Leimbach >> To: bio-linux at nebclists.nerc.ac.uk >> Subject: [Bio-Linux] newest sequin version >> Message-ID: <53E28BA2.206 at uni-wuerzburg.de> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Hi Tim and BL community, >> >> first of all, awesome BL8 release. Runs like a charm on our machines, >> dash bioinfo lens and all, thanks a lot. >> NCBIs sequin is preinstalled in the distro, however I wanted to run a >> newer version. I got the new 64 bit version from NCBIs ftp server: >> >> $ wget ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz >> >> But, it always quits with an error that some library can't be found: >> >> $ ./sequin >> ./sequin: error while loading shared libraries: libjpeg.so.62: cannot >> open shared object file: No such file or directory >> >> Do you guys have an idea how to solve this? I already tried to install >> the old ia32-libs with a work-around, they got disconnected in 13.10 I >> think (I also tried the 32 bit sequin version, misses 'libXm.so.4'). >> Thanks. >> >> Best, >> Andreas >> >> >> -- >> Andreas Leimbach >> Universit?t M?nster >> Institut f?r Hygiene >> Mendelstr. 7 >> D-48149 M?nster >> Germany >> >> Tel.: +49 (0)551 39 33843 >> E-Mail: andreas.leimbach at uni-wuerzburg.de >> > From aleleb at sahfos.ac.uk Mon Aug 11 10:56:10 2014 From: aleleb at sahfos.ac.uk (Alec Colebrook-Clark) Date: Mon, 11 Aug 2014 15:56:10 +0100 Subject: [Bio-Linux] New cluster Message-ID: Hi Tim et all, We are looking at expanding our biolinux infrastructure and implementing a biolinux cluster. The first question I have is would it be better to use a virtual infrastructure than a physical? A colleague has suggested that there is a loss of power with the virtual solution but does it noticeably affect the work being done on biolinux? Secondly, is there any advice on a backup solution. We currently have a 4TB HDD in our biolinux and back it up using the dump command to an external HDD. This was sufficient until we started peaking at 3TB of data. This causes a problem with uncompressing our dump file as we don't have enough space. Thanks in advance Alec -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Mon Aug 11 12:04:34 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 11 Aug 2014 17:04:34 +0100 Subject: [Bio-Linux] New cluster In-Reply-To: References: Message-ID: <53E8E992.6010108@abdn.ac.uk> On 11/08/14 15:56, Alec Colebrook-Clark wrote: > Hi Tim et all, > > > > We are looking at expanding our biolinux infrastructure and implementing > a biolinux cluster. The first question I have is would it be better to > use a virtual infrastructure than a physical? A colleague has suggested > that there is a loss of power with the virtual solution but does it > noticeably affect the work being done on biolinux? Hi, Alec. That depends what your objectives are: Aggregating the resources of multiple machines into a traditional HPC Beowulf cluster or providing virtual equivalents of individual workstations in a private cloud. I ran a Beowulf as a Bio-Linux 7 "x2go" terminal server using "Onesis" for stateless node provision: http://onesis.org/ I also took part in an OpenStack private cloud pilot at the University of Edinburgh and before that I installed Eucalyptus on my Beowulf. It's a lot simpler to run Bio-Linux as a terminal server on bare metal. However, if your users each want their own instance of Bio-Linux to set up and use exactly as they want to then it might be better to create a private cloud. You can, of course, aggregate virtual machines to create a Beowulf-type cluster on a public/private cloud but I'm not convinced this is a good idea other than for 'embarrassingly' parallel comuting. > Secondly, is there any advice on a backup solution. We currently have a > 4TB HDD in our biolinux and back it up using the dump command to an > external HDD. This was sufficient until we started peaking at 3TB of > data. This causes a problem with uncompressing our dump file as we don?t > have enough space. I wrote the ETOH (Enhanced Towers Of Hanoi) version of Tim's Bio-Linux backup script: I use a rule-of-thumb to have about the same amount of space for backup and active filesystems. The dump compression is about 2:1 and this gives sufficient redundancy for about three months of incremental dumps as long as the deltas are not too large. In that case, I force a level 0 dump. However, I'm experimenting with "btrfs" snapshots now and will give up using dump as soon as I can because it is too specific for the physical device and the ext filesystem. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Thu Aug 14 06:35:44 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 14 Aug 2014 11:35:44 +0100 Subject: [Bio-Linux] newest sequin version In-Reply-To: <53E37DA8.2000706@uni-wuerzburg.de> References: <53E37DA8.2000706@uni-wuerzburg.de> Message-ID: <1408012544.7724.11.camel@balisaur> Hi Andreas, Just back in the office and checking e-mails. I'm glad you got Sequin working. I had a look and it seems that the latest binary version on the NCBI FTP site is 13.05 from Jan 2014 but the latest source code is 12.21 from 2012, and since the version on Bio-Linux is made from the source download it's not been updated. I think I need to e-mail NCBI for clarification on this. Personally I find EMBL Webin much easier to use and there is no issue with keeping the software updated. Cheers, TIM On Thu, 2014-08-07 at 14:22 +0100, Andreas Leimbach wrote: > Hey Steve, > > that was it, doh. Thanks a lot! > > Cheers, > Andreas > > > -- > Andreas Leimbach > Universit?t M?nster > Institut f?r Hygiene > Mendelstr. 7 > D-48149 M?nster > Germany > > Tel.: +49 (0)551 39 33843 > E-Mail: andreas.leimbach at uni-wuerzburg.de > > On 07.08.2014 15:08, Steve Moss wrote: > > Dear Andreas, > > > > You need to install libjpeg62 (hence the libjpeg.so.62 in the error > > message), perhaps libjpeg62-dev too?: > > > > sudo apt-get install libjpeg62 libjpeg62-dev > > > > Cheers, > > > > Steve > > > > On 7 August 2014 12:00, wrote: > > > >> Date: Wed, 06 Aug 2014 22:10:10 +0200 > >> From: Andreas Leimbach > >> To: bio-linux at nebclists.nerc.ac.uk > >> Subject: [Bio-Linux] newest sequin version > >> Message-ID: <53E28BA2.206 at uni-wuerzburg.de> > >> Content-Type: text/plain; charset=windows-1252; format=flowed > >> > >> Hi Tim and BL community, > >> > >> first of all, awesome BL8 release. Runs like a charm on our machines, > >> dash bioinfo lens and all, thanks a lot. > >> NCBIs sequin is preinstalled in the distro, however I wanted to run a > >> newer version. I got the new 64 bit version from NCBIs ftp server: > >> > >> $ wget ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz > >> > >> But, it always quits with an error that some library can't be found: > >> > >> $ ./sequin > >> ./sequin: error while loading shared libraries: libjpeg.so.62: cannot > >> open shared object file: No such file or directory > >> > >> Do you guys have an idea how to solve this? I already tried to install > >> the old ia32-libs with a work-around, they got disconnected in 13.10 I > >> think (I also tried the 32 bit sequin version, misses 'libXm.so.4'). > >> Thanks. > >> > >> Best, > >> Andreas > >> > >> > >> -- > >> Andreas Leimbach > >> Universit?t M?nster > >> Institut f?r Hygiene > >> Mendelstr. 7 > >> D-48149 M?nster > >> Germany > >> > >> Tel.: +49 (0)551 39 33843 > >> E-Mail: andreas.leimbach at uni-wuerzburg.de > >> > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From andreas.leimbach at uni-wuerzburg.de Thu Aug 14 07:17:42 2014 From: andreas.leimbach at uni-wuerzburg.de (Andreas Leimbach) Date: Thu, 14 Aug 2014 13:17:42 +0200 Subject: [Bio-Linux] newest sequin version In-Reply-To: <1408012544.7724.11.camel@balisaur> References: <53E37DA8.2000706@uni-wuerzburg.de> <1408012544.7724.11.camel@balisaur> Message-ID: <53EC9AD6.2080501@uni-wuerzburg.de> Hi Tim, thanks for following up. Actually, I don't even know where you can find the source code. I only see binaries. But as you said it's weird, if I browse the FTP site (ftp://ftp.ncbi.nih.gov/sequin/) with Firefox I can see the binaries are last modified "12.02.2012". But if I klick on "CURRENT" (ftp://ftp.ncbi.nih.gov/sequin/CURRENT/) the files are from "30.01.2014". If I download either, it's the same file, version 13.05 ... Sadly, there are many other places NCBI's FTP server is confusing. We're used to Sequin here, but you're right I wanted to switch to EMBL for a long time, maybe now I'll have enough motivation. Best, Andreas -- Andreas Leimbach Universit?t M?nster Institut f?r Hygiene Mendelstr. 7 D-48149 M?nster Germany Tel.: +49 (0)551 39 33843 E-Mail: andreas.leimbach at uni-wuerzburg.de On 14.08.2014 12:35, Tim Booth wrote: > Hi Andreas, > > Just back in the office and checking e-mails. I'm glad you got Sequin > working. I had a look and it seems that the latest binary version on > the NCBI FTP site is 13.05 from Jan 2014 but the latest source code is > 12.21 from 2012, and since the version on Bio-Linux is made from the > source download it's not been updated. I think I need to e-mail NCBI > for clarification on this. > > Personally I find EMBL Webin much easier to use and there is no issue > with keeping the software updated. > > Cheers, > > TIM > > On Thu, 2014-08-07 at 14:22 +0100, Andreas Leimbach wrote: >> Hey Steve, >> >> that was it, doh. Thanks a lot! >> >> Cheers, >> Andreas >> >> >> -- >> Andreas Leimbach >> Universit?t M?nster >> Institut f?r Hygiene >> Mendelstr. 7 >> D-48149 M?nster >> Germany >> >> Tel.: +49 (0)551 39 33843 >> E-Mail: andreas.leimbach at uni-wuerzburg.de >> >> On 07.08.2014 15:08, Steve Moss wrote: >>> Dear Andreas, >>> >>> You need to install libjpeg62 (hence the libjpeg.so.62 in the error >>> message), perhaps libjpeg62-dev too?: >>> >>> sudo apt-get install libjpeg62 libjpeg62-dev >>> >>> Cheers, >>> >>> Steve >>> >>> On 7 August 2014 12:00, wrote: >>> >>>> Date: Wed, 06 Aug 2014 22:10:10 +0200 >>>> From: Andreas Leimbach >>>> To: bio-linux at nebclists.nerc.ac.uk >>>> Subject: [Bio-Linux] newest sequin version >>>> Message-ID: <53E28BA2.206 at uni-wuerzburg.de> >>>> Content-Type: text/plain; charset=windows-1252; format=flowed >>>> >>>> Hi Tim and BL community, >>>> >>>> first of all, awesome BL8 release. Runs like a charm on our machines, >>>> dash bioinfo lens and all, thanks a lot. >>>> NCBIs sequin is preinstalled in the distro, however I wanted to run a >>>> newer version. I got the new 64 bit version from NCBIs ftp server: >>>> >>>> $ wget ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz >>>> >>>> But, it always quits with an error that some library can't be found: >>>> >>>> $ ./sequin >>>> ./sequin: error while loading shared libraries: libjpeg.so.62: cannot >>>> open shared object file: No such file or directory >>>> >>>> Do you guys have an idea how to solve this? I already tried to install >>>> the old ia32-libs with a work-around, they got disconnected in 13.10 I >>>> think (I also tried the 32 bit sequin version, misses 'libXm.so.4'). >>>> Thanks. >>>> >>>> Best, >>>> Andreas >>>> >>>> >>>> -- >>>> Andreas Leimbach >>>> Universit?t M?nster >>>> Institut f?r Hygiene >>>> Mendelstr. 7 >>>> D-48149 M?nster >>>> Germany >>>> >>>> Tel.: +49 (0)551 39 33843 >>>> E-Mail: andreas.leimbach at uni-wuerzburg.de >>>> >>> >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > From tbooth at ceh.ac.uk Thu Aug 14 09:19:36 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 14 Aug 2014 14:19:36 +0100 Subject: [Bio-Linux] New cluster In-Reply-To: <53E8E992.6010108@abdn.ac.uk> References: <53E8E992.6010108@abdn.ac.uk> Message-ID: <1408022376.7724.59.camel@balisaur> Hi Alec, I'd second what Tony says. Keep it as simple as possible and worry more about the loss of your time to set up and maintain a complex system than the loss of "power" from different configurations. Modern enterprise virtualisation does not use much overhead compared to bare metal but it does add another level of complexity to the set-up, so only use it if you need the flexibility. When you say "[lack of space] causes a problem with uncompressing our dump file", I though the "restore" command did all the decompression on-the-fly in RAM and didn't require spare space? Or am I mis-remembering? I've not had to use it in years as we have on-line backups here. Where exactly in the process do you hit problems? Cheers, TIM On Mon, 2014-08-11 at 17:04 +0100, Tony Travis wrote: > On 11/08/14 15:56, Alec Colebrook-Clark wrote: > > Hi Tim et all, > > > > > > > > We are looking at expanding our biolinux infrastructure and implementing > > a biolinux cluster. The first question I have is would it be better to > > use a virtual infrastructure than a physical? A colleague has suggested > > that there is a loss of power with the virtual solution but does it > > noticeably affect the work being done on biolinux? > > Hi, Alec. > > That depends what your objectives are: Aggregating the resources of > multiple machines into a traditional HPC Beowulf cluster or providing > virtual equivalents of individual workstations in a private cloud. > > I ran a Beowulf as a Bio-Linux 7 "x2go" terminal server using "Onesis" > for stateless node provision: > > http://onesis.org/ > > I also took part in an OpenStack private cloud pilot at the University > of Edinburgh and before that I installed Eucalyptus on my Beowulf. > > It's a lot simpler to run Bio-Linux as a terminal server on bare metal. > However, if your users each want their own instance of Bio-Linux to set > up and use exactly as they want to then it might be better to create a > private cloud. You can, of course, aggregate virtual machines to create > a Beowulf-type cluster on a public/private cloud but I'm not convinced > this is a good idea other than for 'embarrassingly' parallel comuting. > > > Secondly, is there any advice on a backup solution. We currently have a > > 4TB HDD in our biolinux and back it up using the dump command to an > > external HDD. This was sufficient until we started peaking at 3TB of > > data. This causes a problem with uncompressing our dump file as we don?t > > have enough space. > > I wrote the ETOH (Enhanced Towers Of Hanoi) version of Tim's Bio-Linux > backup script: I use a rule-of-thumb to have about the same amount of > space for backup and active filesystems. The dump compression is about > 2:1 and this gives sufficient redundancy for about three months of > incremental dumps as long as the deltas are not too large. In that case, > I force a level 0 dump. However, I'm experimenting with "btrfs" > snapshots now and will give up using dump as soon as I can because it is > too specific for the physical device and the ext filesystem. > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at abdn.ac.uk Thu Aug 14 09:59:54 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 14 Aug 2014 14:59:54 +0100 Subject: [Bio-Linux] New cluster In-Reply-To: <1408022376.7724.59.camel@balisaur> References: <53E8E992.6010108@abdn.ac.uk> <1408022376.7724.59.camel@balisaur> Message-ID: <53ECC0DA.2010904@abdn.ac.uk> On 14/08/14 14:19, Tim Booth wrote: > [...] > When you say "[lack of space] causes a problem with uncompressing our > dump file", I though the "restore" command did all the decompression > on-the-fly in RAM and didn't require spare space? Or am I > mis-remembering? I've not had to use it in years as we have on-line > backups here. Where exactly in the process do you hit problems? Hi, Tim and Alec. Tim is right that "restore" can uncompress on the fly (or read a pipe), but unless you are restoring 'in-place' you need somewhere to store the extracted files - e.g. to restore "filename" to /var/tmp from a level 0 backup of /home mounted on /dev/md1p4:: mount /backups cd /var/tmp restore -if /backups/md1p4.bak.0 add filename ... extract This approach means that you can search interactively for the files you want to recover in the dump index and only extract those files. You can also restore files in place if you are *sure* you are not going to overwrite files you want to keep. e.g. to restore "filename" in place: mount /backups cd /home restore -if /backups/md1p4.bak.0 add filename ... extract HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Thu Aug 14 12:59:28 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 14 Aug 2014 17:59:28 +0100 Subject: [Bio-Linux] x2go client on Mac Message-ID: <1408035568.7724.133.camel@balisaur> Hi, While up in Liverpool with Simon earlier this week, we had some issues getting x2go client working properly on a MacBook running "Mountain Lion", but in the end it seemed to work nicely. In particular, it appeared faster than the old FreeNX and was reliably disconnecting and reconnecting sessions, which was reassuring. I thought I'd share what we found... 1. Fullscreen wasn't working, and this seemed to be an issue with XQuartz rather than x2go. If you are seeing just a black screen, try disabling "root window" in XQuartz. 2. Disable shared folders completely in x2go. Leaving this on caused various problems including "key error" messages and sessions freezing. It may well be possible to fix and make it work but you can always transfer your data via SFTP. 3. We had problems with scrambled keymaps, so typing would result in garbage in an editor or terminal. The solution seemed to be (a) enable "follow system keyboard layout" in xquartz and (b) in the top right corner of the MATE desktop, right-click the keyboard icon and under preferences remove all the unwanted input methods and layouts. ( ie, XQuartz on the Mac should be worrying about keyboard settings, not Linux ) Also, as Tony Travis pointed out, the default font sizes in MATE do not look good when viewed in x2go. It's hard for me to pick a good global default, but you can easily set what works best for you under System->Preferences->Appearance->Fonts. If anyone else has issues with x2go, or tips to make it work better, I'd be interested to hear. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From Simon.Wagstaff at liverpool.ac.uk Thu Aug 14 13:05:14 2014 From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon) Date: Thu, 14 Aug 2014 17:05:14 +0000 Subject: [Bio-Linux] x2go client on Mac In-Reply-To: <1408035568.7724.133.camel@balisaur> References: <1408035568.7724.133.camel@balisaur> Message-ID: Thanks Tim. Just a minor point of clarification that should make little difference - it was running OSX 10.9 "Mavericks". Agree, worth the effort as much better than NX Player. Cheers, Simon Sent from my iPhone. Please forgive the curt message and any spelling or grammatical errors. > On 14 Aug 2014, at 17:59, "Tim Booth" wrote: > > Hi, > > While up in Liverpool with Simon earlier this week, we had some issues > getting x2go client working properly on a MacBook running "Mountain > Lion", but in the end it seemed to work nicely. In particular, it > appeared faster than the old FreeNX and was reliably disconnecting and > reconnecting sessions, which was reassuring. I thought I'd share what > we found... > > 1. Fullscreen wasn't working, and this seemed to be an issue with > XQuartz rather than x2go. If you are seeing just a black screen, > try disabling "root window" in XQuartz. > 2. Disable shared folders completely in x2go. Leaving this on > caused various problems including "key error" messages and > sessions freezing. It may well be possible to fix and make it > work but you can always transfer your data via SFTP. > 3. We had problems with scrambled keymaps, so typing would result > in garbage in an editor or terminal. The solution seemed to be > (a) enable "follow system keyboard layout" in xquartz and (b) in > the top right corner of the MATE desktop, right-click the > keyboard icon and under preferences remove all the unwanted > input methods and layouts. > ( ie, XQuartz on the Mac should be worrying about keyboard settings, not Linux ) > > Also, as Tony Travis pointed out, the default font sizes in MATE do not > look good when viewed in x2go. It's hard for me to pick a good global > default, but you can easily set what works best for you under > System->Preferences->Appearance->Fonts. > > If anyone else has issues with x2go, or tips to make it work better, I'd > be interested to hear. > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tony.travis at abdn.ac.uk Thu Aug 14 15:57:33 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 14 Aug 2014 20:57:33 +0100 Subject: [Bio-Linux] x2go client on Mac In-Reply-To: <1408035568.7724.133.camel@balisaur> References: <1408035568.7724.133.camel@balisaur> Message-ID: <53ED14AD.6030606@abdn.ac.uk> On 14/08/14 17:59, Tim Booth wrote: > [...] > Also, as Tony Travis pointed out, the default font sizes in MATE do not > look good when viewed in x2go. It's hard for me to pick a good global > default, but you can easily set what works best for you under > System->Preferences->Appearance->Fonts. Hi, Tim. The main problem is that MATE defaults to 75 dpi, but the hinting in the font rendering is also too agressive. I use the GUI setup from the Menu at the top of the MATE Desktop window in "x2go" to choose fonts: System / Preferences / Appearance / Fonts Application font: [Ubuntu Medium | 11] Document font: [Ubuntu Medium | 11] Desktop font: [ Sans | 11] Window font: [ Ubuntu Light | 11] Fixed Width font: [ Ubuntu Mono | 12] System / Preferences / Appearance / Fonts/ Details Resolution: [96] dots per inch Smoothing (o) Subpixel (LCDs) Hinting (o) Slight Subpixel Order (o) VBGR (default) This gives fonts that look similar to the default Unity Desktop. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From jm at iehinc.com Mon Aug 18 16:39:26 2014 From: jm at iehinc.com (James Mategko) Date: Mon, 18 Aug 2014 13:39:26 -0700 Subject: [Bio-Linux] Qiime Support packages missing? Message-ID: <53F2647E.7080308@iehinc.com> Hello Bio-Linux community, Our lab group has started using Qiime and found that some of the dependencies present in the Qiime Virtual Box are not present in the Bio-Linux install for version 7 or 8. Specific example: bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py -f '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' -r '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' -o '/home/bl8-beta/Desktop/qiimeTests' [sudo] password for bl8-beta: Traceback (most recent call last): File "/usr/lib/qiime/bin/join_paired_ends.py", line 168, in main() File "/usr/lib/qiime/bin/join_paired_ends.py", line 144, in main working_dir = output_dir) File "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/fastq_join.py", line 179, in join_paired_end_reads_fastqjoin HALT_EXEC=HALT_EXEC) File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, in __init__ self._error_on_missing_application(params) File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 434, in _error_on_missing_application % command cogent.app.util.ApplicationNotFoundError: Cannot find fastq-join. Is it installed? Is it in your path? bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py -f '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' -r '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' -o '/home/bl8-beta/Desktop/qiimeTests' The "join_paired_ends.py" feature is dependent on "fastq-join". I searched my BL8 install for "fastq-join" and found no hits. However, in the Qiime Virtual Box the above command works perfectly and "fastq-join" is located in "/home/qiime/qiime_software/ea-utils-1.1.2-537-release". I searched for a few other tools in this directory and they are also not present in BL8 or BL7. It looks like BL's install of qiime was manual rather then a qiime-deploy installation, and the directory ea-utils-1.1.2-537-release was not installed in BL. Our current solution is to use the Qiime VM or reinstall Qiime with qiime-deploy. Is their a less cumbersome solution to get the above command working? Is there a reasion why "ea-utils-1.1.2-537-release "dir is not included in the current copy of BL8? Thank You, - James From tbooth at ceh.ac.uk Tue Aug 19 09:36:55 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 19 Aug 2014 14:36:55 +0100 Subject: [Bio-Linux] Galaxy updates on Bio-Linux Message-ID: <1408455415.7724.265.camel@balisaur> Dear All, A few people have reported significant issues with Galaxy Server after upgrading to Bio-Linux 8. Galaxy is big and complex, has a large number of dependencies, and is being rapidly developed, so maintaining it on Bio-Linux is always going to be a challenge. However I have now updated the packages and made several modifications and run through various tests, so I hope that the result, while not perfect, will be a marked improvement. In particular, installing tools via the "Tool Shed" should now work properly. For example, I've run through the Galaxy 101 at https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need to install the "join on genomic intervals" tool from the tool shed. It complains it can't auto-install bx_python, but then it works anyway as bx_python is already in the core Galaxy package. You can also use the new reference data management features as described here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 At the moment I've included the UCSC genome importer and the BWA index builder by default. Others can be installed via the Tool Shed. I've also put a new documentation page up at http://environmentalomics.org/bio-linux-galaxy explaining how Galaxy is installed on Bio-Linux and how and why this differs from the "standard" config described on the Galaxy website. One particular thing I'm still working to address is that Galaxy on Bio-Linux refuses to import saved histories. I'm not sure why this is right now. Export seems to be OK. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Tue Aug 19 11:08:01 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 19 Aug 2014 16:08:01 +0100 Subject: [Bio-Linux] Qiime Support packages missing? In-Reply-To: <53F2647E.7080308@iehinc.com> References: <53F2647E.7080308@iehinc.com> Message-ID: <1408460881.7724.277.camel@balisaur> Hi James, There are a few dependencies missing on Bio-Linux QIIME compared to the Virtual Box version, and a few of the tool dependencies are not the stipulated versions that QIIME says to use. You are right that qiime-deploy is a cumbersome solution and that's why QIIME on Bio-Linux is installed via versions of the Debian Med packages - see https://packages.debian.org/source/sid/qiime This enables everyone to get updates to QIIME from the system Update Manager, but it does also mean the QIIME system is not identical to the one you get by running qiime-deploy, and also that new dependencies have to be manually added as packages. In the case of ea-utils, I'd not prioritised adding it as "print_qiime_config -t" doesn't ask for it and no other QIIME users have asked me for it either, but you are right it does look like something we need. I'll add it to the package repo now. Cheers, TIM On Mon, 2014-08-18 at 21:39 +0100, James Mategko wrote: > Hello Bio-Linux community, > > Our lab group has started using Qiime and found that some of the > dependencies present in the Qiime Virtual Box are not present in the > Bio-Linux install for version 7 or 8. > > Specific example: > > bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py > -f > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' > -r > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' > -o '/home/bl8-beta/Desktop/qiimeTests' > [sudo] password for bl8-beta: > Traceback (most recent call last): > File "/usr/lib/qiime/bin/join_paired_ends.py", line 168, in > main() > File "/usr/lib/qiime/bin/join_paired_ends.py", line 144, in main > working_dir = output_dir) > File > "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/fastq_join.py", > line 179, in join_paired_end_reads_fastqjoin > HALT_EXEC=HALT_EXEC) > File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, > in __init__ > self._error_on_missing_application(params) > File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 434, > in _error_on_missing_application > % command > cogent.app.util.ApplicationNotFoundError: Cannot find fastq-join. Is it > installed? Is it in your path? > bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py > -f > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' > -r > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' > -o '/home/bl8-beta/Desktop/qiimeTests' > > The "join_paired_ends.py" feature is dependent on "fastq-join". I > searched my BL8 install for "fastq-join" and found no hits. However, in > the Qiime Virtual Box the above command works perfectly and "fastq-join" > is located in "/home/qiime/qiime_software/ea-utils-1.1.2-537-release". I > searched for a few other tools in this directory and they are also not > present in BL8 or BL7. > > It looks like BL's install of qiime was manual rather then a > qiime-deploy installation, and the directory ea-utils-1.1.2-537-release > was not installed in BL. Our current solution is to use the Qiime VM or > reinstall Qiime with qiime-deploy. > > Is their a less cumbersome solution to get the above command working? Is > there a reasion why "ea-utils-1.1.2-537-release "dir is not included in > the current copy of BL8? > > Thank You, > - James > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tilahun.abebe at uni.edu Tue Aug 19 11:59:04 2014 From: tilahun.abebe at uni.edu (Tilahun Abebe) Date: Tue, 19 Aug 2014 10:59:04 -0500 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: <1408455415.7724.265.camel@balisaur> References: <1408455415.7724.265.camel@balisaur> Message-ID: Tim and the Bio-Linux Community, Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux and run the command "galaxy-add-administrator". It looks like the command worked this time. However, I see another unrelated problem when I started Galaxy. The top Galaxy menu bar, which lists administrator, users, shared files, etc is not visible anymore. Is there any thing I need to do other than adding the administrator e-mail address in the configuration "universe_wsgi.ini" file? Thanks. Tilahun On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth wrote: > Dear All, > > A few people have reported significant issues with Galaxy Server after > upgrading to Bio-Linux 8. Galaxy is big and complex, has a large number > of dependencies, and is being rapidly developed, so maintaining it on > Bio-Linux is always going to be a challenge. However I have now updated > the packages and made several modifications and run through various > tests, so I hope that the result, while not perfect, will be a marked > improvement. > > In particular, installing tools via the "Tool Shed" should now work > properly. For example, I've run through the Galaxy 101 at > https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need to > install the "join on genomic intervals" tool from the tool shed. It > complains it can't auto-install bx_python, but then it works anyway as > bx_python is already in the core Galaxy package. > > You can also use the new reference data management features as described > here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 > At the moment I've included the UCSC genome importer and the BWA index > builder by default. Others can be installed via the Tool Shed. > > I've also put a new documentation page up at > http://environmentalomics.org/bio-linux-galaxy explaining how Galaxy is > installed on Bio-Linux and how and why this differs from the "standard" > config described on the Galaxy website. > > One particular thing I'm still working to address is that Galaxy on > Bio-Linux refuses to import saved histories. I'm not sure why this is > right now. Export seems to be OK. > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Aug 19 12:14:07 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 19 Aug 2014 17:14:07 +0100 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: References: <1408455415.7724.265.camel@balisaur> Message-ID: <1408464847.7724.279.camel@balisaur> Hi, Oh dear, I just tried clearing out my browser cache and I get the same problem. I don't know what I changed that would have caused that, but I'll try and fix it. Sorry about that. TIM On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote: > Tim and the Bio-Linux Community, > > > Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux > and run the command "galaxy-add-administrator". It looks like the > command worked this time. However, I see another unrelated problem > when I started Galaxy. The top Galaxy menu bar, which lists > administrator, users, shared files, etc is not visible anymore. Is > there any thing I need to do other than adding the administrator > e-mail address in the configuration "universe_wsgi.ini" file? > > > Thanks. > > > Tilahun > > > > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth wrote: > Dear All, > > A few people have reported significant issues with Galaxy > Server after > upgrading to Bio-Linux 8. Galaxy is big and complex, has a > large number > of dependencies, and is being rapidly developed, so > maintaining it on > Bio-Linux is always going to be a challenge. However I have > now updated > the packages and made several modifications and run through > various > tests, so I hope that the result, while not perfect, will be a > marked > improvement. > > In particular, installing tools via the "Tool Shed" should now > work > properly. For example, I've run through the Galaxy 101 at > https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need > to > install the "join on genomic intervals" tool from the tool > shed. It > complains it can't auto-install bx_python, but then it works > anyway as > bx_python is already in the core Galaxy package. > > You can also use the new reference data management features as > described > here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 > At the moment I've included the UCSC genome importer and the > BWA index > builder by default. Others can be installed via the Tool > Shed. > > I've also put a new documentation page up at > http://environmentalomics.org/bio-linux-galaxy explaining how > Galaxy is > installed on Bio-Linux and how and why this differs from the > "standard" > config described on the Galaxy website. > > One particular thing I'm still working to address is that > Galaxy on > Bio-Linux refuses to import saved histories. I'm not sure why > this is > right now. Export seems to be OK. > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Tue Aug 19 12:54:33 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 19 Aug 2014 17:54:33 +0100 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: References: <1408455415.7724.265.camel@balisaur> Message-ID: <1408467273.7724.292.camel@balisaur> Hi, It turns out that the package didn't build properly on Launchpad.net, which hosts the package repository. Normally this would have triggered an error but in this case it just made a broken package and I didn't notice as my local build had worked and I had the working files still in the browser cache. In any case I believe the issue is rectified. Please install all updates and try again. Cheers, TIM On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote: > Tim and the Bio-Linux Community, > > > Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux > and run the command "galaxy-add-administrator". It looks like the > command worked this time. However, I see another unrelated problem > when I started Galaxy. The top Galaxy menu bar, which lists > administrator, users, shared files, etc is not visible anymore. Is > there any thing I need to do other than adding the administrator > e-mail address in the configuration "universe_wsgi.ini" file? > > > Thanks. > > > Tilahun > > > > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth wrote: > Dear All, > > A few people have reported significant issues with Galaxy > Server after > upgrading to Bio-Linux 8. Galaxy is big and complex, has a > large number > of dependencies, and is being rapidly developed, so > maintaining it on > Bio-Linux is always going to be a challenge. However I have > now updated > the packages and made several modifications and run through > various > tests, so I hope that the result, while not perfect, will be a > marked > improvement. > > In particular, installing tools via the "Tool Shed" should now > work > properly. For example, I've run through the Galaxy 101 at > https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need > to > install the "join on genomic intervals" tool from the tool > shed. It > complains it can't auto-install bx_python, but then it works > anyway as > bx_python is already in the core Galaxy package. > > You can also use the new reference data management features as > described > here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 > At the moment I've included the UCSC genome importer and the > BWA index > builder by default. Others can be installed via the Tool > Shed. > > I've also put a new documentation page up at > http://environmentalomics.org/bio-linux-galaxy explaining how > Galaxy is > installed on Bio-Linux and how and why this differs from the > "standard" > config described on the Galaxy website. > > One particular thing I'm still working to address is that > Galaxy on > Bio-Linux refuses to import saved histories. I'm not sure why > this is > right now. Export seems to be OK. > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Wed Aug 20 07:16:51 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 20 Aug 2014 12:16:51 +0100 Subject: [Bio-Linux] Qiime Support packages missing? In-Reply-To: <53F2647E.7080308@iehinc.com> References: <53F2647E.7080308@iehinc.com> Message-ID: <1408533411.5769.33.camel@balisaur> Dear all, I've now added ea-utils to Bio-Linux. The next update to QIIME will bring in the extra package, or else you can just "apt-get install ea-utils" if you want to join your paired-end sequences right now. This gets the join_paired_ends feature in QIIME working. You might also find the tools useful in themselves - see: https://code.google.com/p/ea-utils/ Mostly I'll pick up missing things like this by running the QIIME self-tests, but annoyingly the "tests/test_join_paired_ends.py" regression test says "All OK" even if fastq-join is not available on the system. For reasons like this, I do appreciate users letting me know when things are amiss. Cheers, TIM On Mon, 2014-08-18 at 21:39 +0100, James Mategko wrote: > Hello Bio-Linux community, > > Our lab group has started using Qiime and found that some of the > dependencies present in the Qiime Virtual Box are not present in the > Bio-Linux install for version 7 or 8. > > Specific example: > > bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py > -f > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' > -r > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' > -o '/home/bl8-beta/Desktop/qiimeTests' > [sudo] password for bl8-beta: > Traceback (most recent call last): > File "/usr/lib/qiime/bin/join_paired_ends.py", line 168, in > main() > File "/usr/lib/qiime/bin/join_paired_ends.py", line 144, in main > working_dir = output_dir) > File > "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/fastq_join.py", > line 179, in join_paired_end_reads_fastqjoin > HALT_EXEC=HALT_EXEC) > File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, > in __init__ > self._error_on_missing_application(params) > File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 434, > in _error_on_missing_application > % command > cogent.app.util.ApplicationNotFoundError: Cannot find fastq-join. Is it > installed? Is it in your path? > bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py > -f > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' > -r > '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' > -o '/home/bl8-beta/Desktop/qiimeTests' > > The "join_paired_ends.py" feature is dependent on "fastq-join". I > searched my BL8 install for "fastq-join" and found no hits. However, in > the Qiime Virtual Box the above command works perfectly and "fastq-join" > is located in "/home/qiime/qiime_software/ea-utils-1.1.2-537-release". I > searched for a few other tools in this directory and they are also not > present in BL8 or BL7. > > It looks like BL's install of qiime was manual rather then a > qiime-deploy installation, and the directory ea-utils-1.1.2-537-release > was not installed in BL. Our current solution is to use the Qiime VM or > reinstall Qiime with qiime-deploy. > > Is their a less cumbersome solution to get the above command working? Is > there a reasion why "ea-utils-1.1.2-537-release "dir is not included in > the current copy of BL8? > > Thank You, > - James > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tilahun.abebe at uni.edu Wed Aug 20 09:52:06 2014 From: tilahun.abebe at uni.edu (Tilahun Abebe) Date: Wed, 20 Aug 2014 08:52:06 -0500 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: <1408467273.7724.292.camel@balisaur> References: <1408455415.7724.265.camel@balisaur> <1408467273.7724.292.camel@balisaur> Message-ID: Hi Tim, Bio-Linux is updated but there is still no change in the appearance of Galaxy. The Galaxy menu (analyze data, shared data, administrator, users) is not visible. I don't even see the Galaxy logo that is normally visible on the left corner of the menu bar. The menu bar is all black. Thanks. Tilahun On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth wrote: > Hi, > > It turns out that the package didn't build properly on Launchpad.net, > which hosts the package repository. Normally this would have triggered > an error but in this case it just made a broken package and I didn't > notice as my local build had worked and I had the working files still in > the browser cache. > > In any case I believe the issue is rectified. Please install all > updates and try again. > > Cheers, > > TIM > > On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote: > > Tim and the Bio-Linux Community, > > > > > > Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux > > and run the command "galaxy-add-administrator". It looks like the > > command worked this time. However, I see another unrelated problem > > when I started Galaxy. The top Galaxy menu bar, which lists > > administrator, users, shared files, etc is not visible anymore. Is > > there any thing I need to do other than adding the administrator > > e-mail address in the configuration "universe_wsgi.ini" file? > > > > > > Thanks. > > > > > > Tilahun > > > > > > > > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth wrote: > > Dear All, > > > > A few people have reported significant issues with Galaxy > > Server after > > upgrading to Bio-Linux 8. Galaxy is big and complex, has a > > large number > > of dependencies, and is being rapidly developed, so > > maintaining it on > > Bio-Linux is always going to be a challenge. However I have > > now updated > > the packages and made several modifications and run through > > various > > tests, so I hope that the result, while not perfect, will be a > > marked > > improvement. > > > > In particular, installing tools via the "Tool Shed" should now > > work > > properly. For example, I've run through the Galaxy 101 at > > https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need > > to > > install the "join on genomic intervals" tool from the tool > > shed. It > > complains it can't auto-install bx_python, but then it works > > anyway as > > bx_python is already in the core Galaxy package. > > > > You can also use the new reference data management features as > > described > > here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 > > At the moment I've included the UCSC genome importer and the > > BWA index > > builder by default. Others can be installed via the Tool > > Shed. > > > > I've also put a new documentation page up at > > http://environmentalomics.org/bio-linux-galaxy explaining how > > Galaxy is > > installed on Bio-Linux and how and why this differs from the > > "standard" > > config described on the Galaxy website. > > > > One particular thing I'm still working to address is that > > Galaxy on > > Bio-Linux refuses to import saved histories. I'm not sure why > > this is > > right now. Export seems to be OK. > > > > Cheers, > > > > TIM > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tilahun.abebe at uni.edu Wed Aug 20 10:20:17 2014 From: tilahun.abebe at uni.edu (Tilahun Abebe) Date: Wed, 20 Aug 2014 09:20:17 -0500 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: References: <1408455415.7724.265.camel@balisaur> <1408467273.7724.292.camel@balisaur> Message-ID: Tim, I was trying different web browsers other than the default Firefox to see if the problem I mentioned is browser-related. I opened Galaxy from Google Chrome and it is working. I can see the Galaxy menu bar with analyze data, shared data, administrator, users, etc. It looks like a small tweaking is needed to open Galaxy on Firefox. Cheers. Tilahun On Wed, Aug 20, 2014 at 8:52 AM, Tilahun Abebe wrote: > Hi Tim, > > Bio-Linux is updated but there is still no change in the appearance of > Galaxy. The Galaxy menu (analyze data, shared data, administrator, users) > is not visible. I don't even see the Galaxy logo that is normally visible > on the left corner of the menu bar. The menu bar is all black. > > Thanks. > > Tilahun > > > On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth wrote: > >> Hi, >> >> It turns out that the package didn't build properly on Launchpad.net, >> which hosts the package repository. Normally this would have triggered >> an error but in this case it just made a broken package and I didn't >> notice as my local build had worked and I had the working files still in >> the browser cache. >> >> In any case I believe the issue is rectified. Please install all >> updates and try again. >> >> Cheers, >> >> TIM >> >> On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe wrote: >> > Tim and the Bio-Linux Community, >> > >> > >> > Thank you for the fix to run Galaxy on Bio-Linux. I updated Bio-Linux >> > and run the command "galaxy-add-administrator". It looks like the >> > command worked this time. However, I see another unrelated problem >> > when I started Galaxy. The top Galaxy menu bar, which lists >> > administrator, users, shared files, etc is not visible anymore. Is >> > there any thing I need to do other than adding the administrator >> > e-mail address in the configuration "universe_wsgi.ini" file? >> > >> > >> > Thanks. >> > >> > >> > Tilahun >> > >> > >> > >> > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth wrote: >> > Dear All, >> > >> > A few people have reported significant issues with Galaxy >> > Server after >> > upgrading to Bio-Linux 8. Galaxy is big and complex, has a >> > large number >> > of dependencies, and is being rapidly developed, so >> > maintaining it on >> > Bio-Linux is always going to be a challenge. However I have >> > now updated >> > the packages and made several modifications and run through >> > various >> > tests, so I hope that the result, while not perfect, will be a >> > marked >> > improvement. >> > >> > In particular, installing tools via the "Tool Shed" should now >> > work >> > properly. For example, I've run through the Galaxy 101 at >> > https://usegalaxy.org/u/aun1/p/galaxy101 and for that you need >> > to >> > install the "join on genomic intervals" tool from the tool >> > shed. It >> > complains it can't auto-install bx_python, but then it works >> > anyway as >> > bx_python is already in the core Galaxy package. >> > >> > You can also use the new reference data management features as >> > described >> > here: http://www.ncbi.nlm.nih.gov/pubmed/24585771 >> > At the moment I've included the UCSC genome importer and the >> > BWA index >> > builder by default. Others can be installed via the Tool >> > Shed. >> > >> > I've also put a new documentation page up at >> > http://environmentalomics.org/bio-linux-galaxy explaining how >> > Galaxy is >> > installed on Bio-Linux and how and why this differs from the >> > "standard" >> > config described on the Galaxy website. >> > >> > One particular thing I'm still working to address is that >> > Galaxy on >> > Bio-Linux refuses to import saved histories. I'm not sure why >> > this is >> > right now. Export seems to be OK. >> > >> > Cheers, >> > >> > TIM >> > >> > -- >> > Tim Booth >> > NERC Environmental Bioinformatics Centre >> > >> > Centre for Ecology and Hydrology >> > Maclean Bldg, Benson Lane >> > Crowmarsh Gifford >> > Wallingford, England >> > OX10 8BB >> > >> > http://nebc.nerc.ac.uk >> > +44 1491 69 2705 >> > _______________________________________________ >> > Bio-Linux mailing list >> > Bio-Linux at nebclists.nerc.ac.uk >> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> > >> > >> >> -- >> Tim Booth >> NERC Environmental Bioinformatics Centre >> >> Centre for Ecology and Hydrology >> Maclean Bldg, Benson Lane >> Crowmarsh Gifford >> Wallingford, England >> OX10 8BB >> >> http://nebc.nerc.ac.uk >> +44 1491 69 2705 >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Aug 20 10:34:03 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 20 Aug 2014 15:34:03 +0100 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: References: <1408455415.7724.265.camel@balisaur> <1408467273.7724.292.camel@balisaur> Message-ID: <1408545243.5769.43.camel@balisaur> Hi Tilahun, Thanks for your persistence. I'm sure I also saw the problem as you describe, and it was due to several Javascript libraries being missed out of the package which explains why the interface could not be drawn. I've confirmed the libraries are back in the latest package, and I have also tested it in both Chrome and Firefox and it now works for me. Are you sure that it is not a caching issue in Firefox? If you hold down "shift" and reload the page that should force a full reload. Does that help at all? Cheers, TIM On Wed, 2014-08-20 at 15:20 +0100, Tilahun Abebe wrote: > Tim, > > > I was trying different web browsers other than the default Firefox to > see if the problem I mentioned is browser-related. I opened Galaxy > from Google Chrome and it is working. I can see the Galaxy menu bar > with analyze data, shared data, administrator, users, etc. It looks > like a small tweaking is needed to open Galaxy on Firefox. > > > Cheers. > > > Tilahun > > > > On Wed, Aug 20, 2014 at 8:52 AM, Tilahun Abebe > wrote: > Hi Tim, > > > Bio-Linux is updated but there is still no change in the > appearance of Galaxy. The Galaxy menu (analyze data, shared > data, administrator, users) is not visible. I don't even see > the Galaxy logo that is normally visible on the left corner of > the menu bar. The menu bar is all black. > > > Thanks. > > > Tilahun > > > > On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth > wrote: > Hi, > > It turns out that the package didn't build properly on > Launchpad.net, > which hosts the package repository. Normally this > would have triggered > an error but in this case it just made a broken > package and I didn't > notice as my local build had worked and I had the > working files still in > the browser cache. > > In any case I believe the issue is rectified. Please > install all > updates and try again. > > Cheers, > > TIM > > On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe > wrote: > > > Tim and the Bio-Linux Community, > > > > > > Thank you for the fix to run Galaxy on Bio-Linux. I > updated Bio-Linux > > and run the command "galaxy-add-administrator". It > looks like the > > command worked this time. However, I see another > unrelated problem > > when I started Galaxy. The top Galaxy menu bar, > which lists > > administrator, users, shared files, etc is not > visible anymore. Is > > there any thing I need to do other than adding the > administrator > > e-mail address in the configuration > "universe_wsgi.ini" file? > > > > > > Thanks. > > > > > > Tilahun > > > > > > > > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth > wrote: > > Dear All, > > > > A few people have reported significant > issues with Galaxy > > Server after > > upgrading to Bio-Linux 8. Galaxy is big and > complex, has a > > large number > > of dependencies, and is being rapidly > developed, so > > maintaining it on > > Bio-Linux is always going to be a challenge. > However I have > > now updated > > the packages and made several modifications > and run through > > various > > tests, so I hope that the result, while not > perfect, will be a > > marked > > improvement. > > > > In particular, installing tools via the > "Tool Shed" should now > > work > > properly. For example, I've run through the > Galaxy 101 at > > https://usegalaxy.org/u/aun1/p/galaxy101 and > for that you need > > to > > install the "join on genomic intervals" tool > from the tool > > shed. It > > complains it can't auto-install bx_python, > but then it works > > anyway as > > bx_python is already in the core Galaxy > package. > > > > You can also use the new reference data > management features as > > described > > here: > http://www.ncbi.nlm.nih.gov/pubmed/24585771 > > At the moment I've included the UCSC genome > importer and the > > BWA index > > builder by default. Others can be installed > via the Tool > > Shed. > > > > I've also put a new documentation page up at > > > http://environmentalomics.org/bio-linux-galaxy > explaining how > > Galaxy is > > installed on Bio-Linux and how and why this > differs from the > > "standard" > > config described on the Galaxy website. > > > > One particular thing I'm still working to > address is that > > Galaxy on > > Bio-Linux refuses to import saved histories. > I'm not sure why > > this is > > right now. Export seems to be OK. > > > > Cheers, > > > > TIM > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tilahun.abebe at uni.edu Wed Aug 20 10:46:20 2014 From: tilahun.abebe at uni.edu (Tilahun Abebe) Date: Wed, 20 Aug 2014 09:46:20 -0500 Subject: [Bio-Linux] Galaxy updates on Bio-Linux In-Reply-To: <1408545243.5769.43.camel@balisaur> References: <1408455415.7724.265.camel@balisaur> <1408467273.7724.292.camel@balisaur> <1408545243.5769.43.camel@balisaur> Message-ID: Tim, That was so easy. It worked! I will check installing tools from the toolshed and let you know if I have problems. Thank you for all your support. Tilahun On Wed, Aug 20, 2014 at 9:34 AM, Tim Booth wrote: > Hi Tilahun, > > Thanks for your persistence. I'm sure I also saw the problem as you > describe, and it was due to several Javascript libraries being missed > out of the package which explains why the interface could not be drawn. > > I've confirmed the libraries are back in the latest package, and I have > also tested it in both Chrome and Firefox and it now works for me. Are > you sure that it is not a caching issue in Firefox? If you hold down > "shift" and reload the page that should force a full reload. Does that > help at all? > > Cheers, > > TIM > > On Wed, 2014-08-20 at 15:20 +0100, Tilahun Abebe wrote: > > Tim, > > > > > > I was trying different web browsers other than the default Firefox to > > see if the problem I mentioned is browser-related. I opened Galaxy > > from Google Chrome and it is working. I can see the Galaxy menu bar > > with analyze data, shared data, administrator, users, etc. It looks > > like a small tweaking is needed to open Galaxy on Firefox. > > > > > > Cheers. > > > > > > Tilahun > > > > > > > > On Wed, Aug 20, 2014 at 8:52 AM, Tilahun Abebe > > wrote: > > Hi Tim, > > > > > > Bio-Linux is updated but there is still no change in the > > appearance of Galaxy. The Galaxy menu (analyze data, shared > > data, administrator, users) is not visible. I don't even see > > the Galaxy logo that is normally visible on the left corner of > > the menu bar. The menu bar is all black. > > > > > > Thanks. > > > > > > Tilahun > > > > > > > > On Tue, Aug 19, 2014 at 11:54 AM, Tim Booth > > wrote: > > Hi, > > > > It turns out that the package didn't build properly on > > Launchpad.net, > > which hosts the package repository. Normally this > > would have triggered > > an error but in this case it just made a broken > > package and I didn't > > notice as my local build had worked and I had the > > working files still in > > the browser cache. > > > > In any case I believe the issue is rectified. Please > > install all > > updates and try again. > > > > Cheers, > > > > TIM > > > > On Tue, 2014-08-19 at 16:59 +0100, Tilahun Abebe > > wrote: > > > > > Tim and the Bio-Linux Community, > > > > > > > > > Thank you for the fix to run Galaxy on Bio-Linux. I > > updated Bio-Linux > > > and run the command "galaxy-add-administrator". It > > looks like the > > > command worked this time. However, I see another > > unrelated problem > > > when I started Galaxy. The top Galaxy menu bar, > > which lists > > > administrator, users, shared files, etc is not > > visible anymore. Is > > > there any thing I need to do other than adding the > > administrator > > > e-mail address in the configuration > > "universe_wsgi.ini" file? > > > > > > > > > Thanks. > > > > > > > > > Tilahun > > > > > > > > > > > > On Tue, Aug 19, 2014 at 8:36 AM, Tim Booth > > wrote: > > > Dear All, > > > > > > A few people have reported significant > > issues with Galaxy > > > Server after > > > upgrading to Bio-Linux 8. Galaxy is big and > > complex, has a > > > large number > > > of dependencies, and is being rapidly > > developed, so > > > maintaining it on > > > Bio-Linux is always going to be a challenge. > > However I have > > > now updated > > > the packages and made several modifications > > and run through > > > various > > > tests, so I hope that the result, while not > > perfect, will be a > > > marked > > > improvement. > > > > > > In particular, installing tools via the > > "Tool Shed" should now > > > work > > > properly. For example, I've run through the > > Galaxy 101 at > > > https://usegalaxy.org/u/aun1/p/galaxy101 and > > for that you need > > > to > > > install the "join on genomic intervals" tool > > from the tool > > > shed. It > > > complains it can't auto-install bx_python, > > but then it works > > > anyway as > > > bx_python is already in the core Galaxy > > package. > > > > > > You can also use the new reference data > > management features as > > > described > > > here: > > http://www.ncbi.nlm.nih.gov/pubmed/24585771 > > > At the moment I've included the UCSC genome > > importer and the > > > BWA index > > > builder by default. Others can be installed > > via the Tool > > > Shed. > > > > > > I've also put a new documentation page up at > > > > > http://environmentalomics.org/bio-linux-galaxy > > explaining how > > > Galaxy is > > > installed on Bio-Linux and how and why this > > differs from the > > > "standard" > > > config described on the Galaxy website. > > > > > > One particular thing I'm still working to > > address is that > > > Galaxy on > > > Bio-Linux refuses to import saved histories. > > I'm not sure why > > > this is > > > right now. Export seems to be OK. > > > > > > Cheers, > > > > > > TIM > > > > > > -- > > > Tim Booth > > > NERC Environmental Bioinformatics Centre > > > > > > Centre for Ecology and Hydrology > > > Maclean Bldg, Benson Lane > > > Crowmarsh Gifford > > > Wallingford, England > > > OX10 8BB > > > > > > http://nebc.nerc.ac.uk > > > +44 1491 69 2705 > > > > > _______________________________________________ > > > Bio-Linux mailing list > > > Bio-Linux at nebclists.nerc.ac.uk > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm at iehinc.com Thu Aug 21 20:31:10 2014 From: jm at iehinc.com (James Mategko) Date: Thu, 21 Aug 2014 17:31:10 -0700 Subject: [Bio-Linux] Qiime Support packages missing? In-Reply-To: <1408533411.5769.33.camel@balisaur> References: <53F2647E.7080308@iehinc.com> <1408533411.5769.33.camel@balisaur> Message-ID: <53F68F4E.1010706@iehinc.com> Hi Tim, I installed the update in BL8 with apt-get. The qiime command I listed before now works perfectly. Thank You for pushing out the update so rapidly. - James On 8/20/2014 4:16 AM, Tim Booth wrote: > Dear all, > > I've now added ea-utils to Bio-Linux. The next update to QIIME will > bring in the extra package, or else you can just "apt-get install > ea-utils" if you want to join your paired-end sequences right now. This > gets the join_paired_ends feature in QIIME working. You might also find > the tools useful in themselves - see: > > https://code.google.com/p/ea-utils/ > > Mostly I'll pick up missing things like this by running the QIIME > self-tests, but annoyingly the "tests/test_join_paired_ends.py" > regression test says "All OK" even if fastq-join is not available on the > system. For reasons like this, I do appreciate users letting me know > when things are amiss. > > Cheers, > > TIM > > On Mon, 2014-08-18 at 21:39 +0100, James Mategko wrote: >> Hello Bio-Linux community, >> >> Our lab group has started using Qiime and found that some of the >> dependencies present in the Qiime Virtual Box are not present in the >> Bio-Linux install for version 7 or 8. >> >> Specific example: >> >> bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py >> -f >> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' >> -r >> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' >> -o '/home/bl8-beta/Desktop/qiimeTests' >> [sudo] password for bl8-beta: >> Traceback (most recent call last): >> File "/usr/lib/qiime/bin/join_paired_ends.py", line 168, in >> main() >> File "/usr/lib/qiime/bin/join_paired_ends.py", line 144, in main >> working_dir = output_dir) >> File >> "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/fastq_join.py", >> line 179, in join_paired_end_reads_fastqjoin >> HALT_EXEC=HALT_EXEC) >> File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, >> in __init__ >> self._error_on_missing_application(params) >> File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 434, >> in _error_on_missing_application >> % command >> cogent.app.util.ApplicationNotFoundError: Cannot find fastq-join. Is it >> installed? Is it in your path? >> bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py >> -f >> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' >> -r >> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' >> -o '/home/bl8-beta/Desktop/qiimeTests' >> >> The "join_paired_ends.py" feature is dependent on "fastq-join". I >> searched my BL8 install for "fastq-join" and found no hits. However, in >> the Qiime Virtual Box the above command works perfectly and "fastq-join" >> is located in "/home/qiime/qiime_software/ea-utils-1.1.2-537-release". I >> searched for a few other tools in this directory and they are also not >> present in BL8 or BL7. >> >> It looks like BL's install of qiime was manual rather then a >> qiime-deploy installation, and the directory ea-utils-1.1.2-537-release >> was not installed in BL. Our current solution is to use the Qiime VM or >> reinstall Qiime with qiime-deploy. >> >> Is their a less cumbersome solution to get the above command working? Is >> there a reasion why "ea-utils-1.1.2-537-release "dir is not included in >> the current copy of BL8? >> >> Thank You, >> - James >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux