From David.HALFMAERTEN at inbo.be Mon Feb 10 05:47:17 2014 From: David.HALFMAERTEN at inbo.be (HALFMAERTEN, David) Date: Mon, 10 Feb 2014 10:47:17 +0000 Subject: [Bio-Linux] Bio-Linux 7.0.9 stable? Message-ID: Dear Mr. Booth, I would like to try bio-linux and noticed a new release (7.0.9) is available for download but don't find any details about the changes compared to 7.0.7. What are the differences and would you recommend to install 7.0.9 or 7.0.7? Best regards, David [cid:image001.jpg at 01CF2655.D904F490] David Halfmaerten Research Assistant Genetic Diversity Research Institute for Nature and Forest (INBO) Gaverstraat 4, 9500 Geraardsbergen, Belgium tel +32 54 43 61 93 (new!) | mobile +32 479 99 22 02 david.halfmaerten at inbo.be www.inbo.be * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2145 bytes Desc: image001.jpg URL: From tbooth at ceh.ac.uk Mon Feb 10 12:33:39 2014 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Mon, 10 Feb 2014 17:33:39 +0000 Subject: [Bio-Linux] Bio-Linux 7.0.9 stable? In-Reply-To: References: Message-ID: <8C33D34D431A974EAEA913101DDA1944044935A657@nerckwmbc.ad.nerc.ac.uk> Hi David, There's not much difference. The 7.0.9 has some extra packages I added for the purpose of running a course but if you want them you can just add them via Synaptic (taverna-workbench plus panama plus all the r-bioc-* packages). Once the system is installed any packages on there will be updated by the package manager so you don't need to worry about your system being out of date. I've now got a 7.1.0 image that should boot directly on machines that insist on UEFI "secure" boot media. That is, some WIndows 8 machines that don't let you disable the security check or add non-Microsoft keys. I've not put that up yet as I don't have any such machine to test on and I'm now mainly thinking about BL8, but maybe someone on this list could volunteer? Cheers, TIM ________________________________________ From: HALFMAERTEN, David [David.HALFMAERTEN at inbo.be] Sent: 10 February 2014 10:47 To: bio-linux at nebclists.nerc.ac.uk Subject: [Bio-Linux] Bio-Linux 7.0.9 stable? Dear Mr. Booth, I would like to try bio-linux and noticed a new release (7.0.9) is available for download but don?t find any details about the changes compared to 7.0.7. What are the differences and would you recommend to install 7.0.9 or 7.0.7? Best regards, David [cid:image001.jpg at 01CF2655.D904F490] David Halfmaerten Research Assistant Genetic Diversity Research Institute for Nature and Forest (INBO) Gaverstraat 4, 9500 Geraardsbergen, Belgium tel +32 54 43 61 93 (new!) | mobile +32 479 99 22 02 david.halfmaerten at inbo.be www.inbo.be * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tony.travis at abdn.ac.uk Mon Feb 10 12:43:36 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 10 Feb 2014 17:43:36 +0000 Subject: [Bio-Linux] Bio-Linux 7.0.9 stable? In-Reply-To: <8C33D34D431A974EAEA913101DDA1944044935A657@nerckwmbc.ad.nerc.ac.uk> References: <8C33D34D431A974EAEA913101DDA1944044935A657@nerckwmbc.ad.nerc.ac.uk> Message-ID: <52F90FC8.1030201@abdn.ac.uk> On 10/02/14 17:33, Booth, Timothy G. wrote: > [...] > keys. I've not put that up yet as I don't have any such machine to > test on and I'm now mainly thinking about BL8, but maybe someone on > this list could volunteer? Hi, Tim. I could try it out on a MacBook Air if you want? 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. From princess.jasmine.lognnes at gmail.com Tue Feb 11 08:29:24 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Tue, 11 Feb 2014 14:29:24 +0100 Subject: [Bio-Linux] How to Install all packages on Ubuntu? Message-ID: Hello all =) The USB stick fails to boot on my netbook after the boot loader, because it can't recognize the keyboard. So I tried to install ALL the bio-linux packages on a Ubuntu 12.04 64bit, and ran into tons of dependency issues. Have anyone succeed in installing all the packages, and if so, how? =) Hugs, Jasmine -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Feb 11 13:54:29 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 11 Feb 2014 18:54:29 +0000 Subject: [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: Message-ID: <1392144869.5335.3.camel@balisaur> Hi Jasmine, Installing all the bio-linux-* packages listed in the package manager is a bad idea, but you can install all the ones that come on the standard Bio-Linux installation by using the same script I made for Bio-Linux 6->7 upgrades. Please see this page: http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/upgrade6-to-7 Cheers, TIM On Tue, 2014-02-11 at 13:29 +0000, Jasmine Lognnes wrote: > Hello all =) > > > The USB stick fails to boot on my netbook after the boot loader, > because it can't recognize the keyboard. So I tried to install ALL the > bio-linux packages on a Ubuntu 12.04 64bit, and ran into tons of > dependency issues. > > > Have anyone succeed in installing all the packages, and if so, how? =) > > > Hugs, > Jasmine > > > > -- 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 princess.jasmine.lognnes at gmail.com Wed Feb 12 10:03:17 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Wed, 12 Feb 2014 16:03:17 +0100 Subject: [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: <1392144869.5335.3.camel@balisaur> References: <1392144869.5335.3.camel@balisaur> Message-ID: Dear Tim, That's a very impressive script. Wow! By going through the script I have cherry picked what looks like to be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. Can you verify that it is the correct procedure? On the liveUSB I did grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' and got the attached list of packages. On a successful installation, should I end up these exact packages? Hugs, Jasmine =) On 11 February 2014 19:54, Tim Booth wrote: > Hi Jasmine, > > Installing all the bio-linux-* packages listed in the package manager is > a bad idea, but you can install all the ones that come on the standard > Bio-Linux installation by using the same script I made for Bio-Linux > 6->7 upgrades. > > Please see this page: > > http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/upgrade6-to-7 > > Cheers, > > TIM > > On Tue, 2014-02-11 at 13:29 +0000, Jasmine Lognnes wrote: > > Hello all =) > > > > > > The USB stick fails to boot on my netbook after the boot loader, > > because it can't recognize the keyboard. So I tried to install ALL the > > bio-linux packages on a Ubuntu 12.04 64bit, and ran into tons of > > dependency issues. > > > > > > Have anyone succeed in installing all the packages, and if so, how? =) > > > > > > Hugs, > > Jasmine > > > > > > > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: bl7.sh Type: application/x-sh Size: 1215 bytes Desc: not available URL: From tony.travis at abdn.ac.uk Wed Feb 12 10:32:59 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 12 Feb 2014 15:32:59 +0000 Subject: [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> Message-ID: <52FB942B.8070103@abdn.ac.uk> On 12/02/14 15:03, Jasmine Lognnes wrote: > Dear Tim, > > That's a very impressive script. Wow! > > By going through the script I have cherry picked what looks like to be > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > Can you verify that it is the correct procedure? > > On the liveUSB I did > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > and got the attached list of packages. On a successful installation, > should I end up these exact packages? Hi, Jasmine. I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu 12.04 LTS systems without any problems. You don't need to grep things out like you did. Just run the script in its entirety and please email any bug reports to the bio-linux-dev list. 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. From princess.jasmine.lognnes at gmail.com Fri Feb 14 05:29:01 2014 From: princess.jasmine.lognnes at gmail.com (Jasmine Lognnes) Date: Fri, 14 Feb 2014 11:29:01 +0100 Subject: [Bio-Linux] How to Install all packages on Ubuntu? In-Reply-To: References: <1392144869.5335.3.camel@balisaur> <52FB942B.8070103@abdn.ac.uk> Message-ID: Dear Tony, That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this? Hugs, Jasmine =) The following NEW packages will be installed: bio-linux-artemis 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded. Need to get 11.8 MB of archives. After this operation, 47.7 MB of additional disk space will be used. Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis. (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up bio-linux-artemis (15.1.1-1) ... Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package bio-linux-assembly-conversion-tools Not all packages installed properly - exiting. On 12 February 2014 16:32, Tony Travis wrote: > > On 12/02/14 15:03, Jasmine Lognnes wrote: > > Dear Tim, > > > > That's a very impressive script. Wow! > > > > By going through the script I have cherry picked what looks like to be > > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script. > > Can you verify that it is the correct procedure? > > > > On the liveUSB I did > > > > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}' > > > > and got the attached list of packages. On a successful installation, > > should I end up these exact packages? > > Hi, Jasmine. > > I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu > 12.04 LTS systems without any problems. You don't need to grep things > out like you did. Just run the script in its entirety and please email > any bug reports to the bio-linux-dev list. > > 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. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux