From Simon.Wagstaff at liverpool.ac.uk Tue Mar 2 03:55:36 2010 From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon) Date: Tue, 2 Mar 2010 08:55:36 +0000 Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation In-Reply-To: <1DCCED50D0696A498958BA6B254456E20874F92FE7@nerckwmb1.ad.nerc.ac.uk> References: <1DCCED50D0696A498958BA6B254456E20874F92FE7@nerckwmb1.ad.nerc.ac.uk> Message-ID: Hi Bela, My machine won't play ball with the latest update - see below. simonw at pc248014[simonw] su manager [ 8:52AM] Password: manager at pc248014[simonw] sudo apt -get -f install [ 8:52AM] [sudo] password for manager: sudo: apt: command not found Perhaps I've done something wrong? Cheers, Simon ________________________________________ From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Tiwari, Bela [btiwari at ceh.ac.uk] Sent: 25 February 2010 09:21 To: bio-linux at nebc.nox.ac.uk Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation Dear Bio-Linux Users, The newest version of bio-linux-emboss was released late yesterday. Many Bio-Linux systems will have picked up this update overnight. To complete the installation, you will need to log into your system, and run the command sudo apt-get -f install If your machine does not install updates automatically at night, please update your system and then run the above command from a terminal window. This new bio-linux-emboss package changes substantially the way we have been distributing EMBOSS and allows it to be installed on 32 or 64 bit systems. The main changes to be aware of are listed below, in approximate order of importance. Please feel free to write to the NEBC helpdesk (helpdesk at nebc.nox.ac.uk) if you notice any issues with the new package. Overview: bio-linux-emboss is now a wrapper package. It includes the necessary indices for EMBOSS restriction mapping programs, em_pscan for searching prints, patmatmotifs for searching prosite, transcription factor searching using jaspscan, and programs making use of amino acid properties such as pepwindow and pepwindowall. It also includes Jemboss. bio-linux-emboss pulls in the base binaries, documentation and basic data files from Ubuntu packages. The underlying version of EMBOSS on your system is 6.0.1, and should track new versions of EMBOSS as they become available in the Ubuntu repositories. Major changes: If you have edited your emboss.default file in the past, it will be kept and saved to /usr/share/EMBOSS/emboss.default.old. You can replace the distributed version /usr/share/EMBOSS/emboss.default with your old version if you wish. The emboss.default file we distribute in bio-linux-emboss supports fetching sequences from the same databases as it has before: embl, emblcds, refseq and uniprot (also aliased as swissprot and trembl). The pscan and cons programs distributed with the Ubuntu emboss package are called em_pscan and em_cons. This means you will need to call these programs using their new names, and also means that for the moment, these programs are not available through the Jemboss interface. The EMBASSY versions of Phylips software have changed names. They used to use the same name as native Phylip programs, prefaced by an e (for example, eprotpars runs the EMBASSY version of protpars). Now these programs are prefaced by an f (so, for example, fprotpars). Not all the software available as EMBASSY packages is yet available as Ubuntu packages. This means that the following software packages are no longer distributed as part of bio-linux-emboss: emnu, esim4, hmmernew, mira, memenew, signature, structure, and topo. Please note that this only refers to the EMBASSY versions of the software. You can still install bio-linux-hmmer and bio-linux-mira to get the native programs. If you are a user of the EMBASSY versions of the software listed in the paragraph and are concerned about losing these programs, please let us know by emailing helpdesk at nebc.nox.ac.uk The bio-linux-emboss-kmenus package will continue to be available for Bio-Linux 5 systems (based on Ubuntu 8.04). This package provides the graphical interface when Emboss programs are run from the main Bioinformatics menu. This will not work on more recent Ubuntu versions due to an incompatibility with the Kaptain software, and therefore will be removed in Bio-Linux 6. We recommend that people consider using other ways of running the EMBOSS software. For graphical access, we suggest Jemboss, which can be started by typing jemboss on the command line, or by choosing the Jemboss option under the Bioinformatics menu. Another option is to install the web-based package from Ubuntu: emboss-explorer. regards, The NEBC Team ************************* NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk tel: 01491 69 2705 Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB ************************* -- 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 Simon.Wagstaff at liverpool.ac.uk Tue Mar 2 03:59:55 2010 From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon) Date: Tue, 2 Mar 2010 08:59:55 +0000 Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation In-Reply-To: <1DCCED50D0696A498958BA6B254456E20874F92FE7@nerckwmb1.ad.nerc.ac.uk> References: <1DCCED50D0696A498958BA6B254456E20874F92FE7@nerckwmb1.ad.nerc.ac.uk> Message-ID: Sorry - just noticed my typo. Lack of sleep last night. Simon From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Tiwari, Bela Sent: 25 February 2010 09:21 To: bio-linux at nebc.nox.ac.uk Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation Dear Bio-Linux Users, The newest version of bio-linux-emboss was released late yesterday. Many Bio-Linux systems will have picked up this update overnight. To complete the installation, you will need to log into your system, and run the command sudo apt-get -f install If your machine does not install updates automatically at night, please update your system and then run the above command from a terminal window. This new bio-linux-emboss package changes substantially the way we have been distributing EMBOSS and allows it to be installed on 32 or 64 bit systems. The main changes to be aware of are listed below, in approximate order of importance. Please feel free to write to the NEBC helpdesk (helpdesk at nebc.nox.ac.uk) if you notice any issues with the new package. Overview: bio-linux-emboss is now a wrapper package. It includes the necessary indices for EMBOSS restriction mapping programs, em_pscan for searching prints, patmatmotifs for searching prosite, transcription factor searching using jaspscan, and programs making use of amino acid properties such as pepwindow and pepwindowall. It also includes Jemboss. bio-linux-emboss pulls in the base binaries, documentation and basic data files from Ubuntu packages. The underlying version of EMBOSS on your system is 6.0.1, and should track new versions of EMBOSS as they become available in the Ubuntu repositories. Major changes: If you have edited your emboss.default file in the past, it will be kept and saved to /usr/share/EMBOSS/emboss.default.old. You can replace the distributed version /usr/share/EMBOSS/emboss.default with your old version if you wish. The emboss.default file we distribute in bio-linux-emboss supports fetching sequences from the same databases as it has before: embl, emblcds, refseq and uniprot (also aliased as swissprot and trembl). The pscan and cons programs distributed with the Ubuntu emboss package are called em_pscan and em_cons. This means you will need to call these programs using their new names, and also means that for the moment, these programs are not available through the Jemboss interface. The EMBASSY versions of Phylips software have changed names. They used to use the same name as native Phylip programs, prefaced by an e (for example, eprotpars runs the EMBASSY version of protpars). Now these programs are prefaced by an f (so, for example, fprotpars). Not all the software available as EMBASSY packages is yet available as Ubuntu packages. This means that the following software packages are no longer distributed as part of bio-linux-emboss: emnu, esim4, hmmernew, mira, memenew, signature, structure, and topo. Please note that this only refers to the EMBASSY versions of the software. You can still install bio-linux-hmmer and bio-linux-mira to get the native programs. If you are a user of the EMBASSY versions of the software listed in the paragraph and are concerned about losing these programs, please let us know by emailing helpdesk at nebc.nox.ac.uk The bio-linux-emboss-kmenus package will continue to be available for Bio-Linux 5 systems (based on Ubuntu 8.04). This package provides the graphical interface when Emboss programs are run from the main Bioinformatics menu. This will not work on more recent Ubuntu versions due to an incompatibility with the Kaptain software, and therefore will be removed in Bio-Linux 6. We recommend that people consider using other ways of running the EMBOSS software. For graphical access, we suggest Jemboss, which can be started by typing jemboss on the command line, or by choosing the Jemboss option under the Bioinformatics menu. Another option is to install the web-based package from Ubuntu: emboss-explorer. regards, The NEBC Team ************************* NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk tel: 01491 69 2705 Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB ************************* -- 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinformatics.lists at gmail.com Tue Mar 2 06:02:00 2010 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Tue, 2 Mar 2010 11:02:00 +0000 Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation In-Reply-To: References: <1DCCED50D0696A498958BA6B254456E20874F92FE7@nerckwmb1.ad.nerc.ac.uk> Message-ID: Simon, it looks like there's a space between apt and -get in your command it should be sudo apt-get -f install there is no space in 'apt-get' :) - but there is one between 'apt-get' '-f' and 'install' regards, Dan On 2 March 2010 08:55, Wagstaff, Simon wrote: > Hi Bela, > > My machine won't play ball with the latest update - see below. > > simonw at pc248014[simonw] su manager ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?[ 8:52AM] > Password: > manager at pc248014[simonw] sudo apt -get -f install ? ? ? ? ? ? ? ? ? ? [ 8:52AM] > [sudo] password for manager: > sudo: apt: command not found > > Perhaps I've done something wrong? > > Cheers, > > Simon > > ________________________________________ > From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Tiwari, Bela [btiwari at ceh.ac.uk] > Sent: 25 February 2010 09:21 > To: bio-linux at nebc.nox.ac.uk > Subject: [Bio-Linux] new bio-linux-emboss and how to complete installation > > Dear Bio-Linux Users, > > > > The newest version of bio-linux-emboss was released late yesterday. Many Bio-Linux systems will have picked up this update overnight. To complete the installation, you will need to log into your system, and run the command > > > > sudo apt-get -f install > > > > If your machine does not install updates automatically at night, please update your system and then run the above command from a terminal window. > > > > This new bio-linux-emboss package changes substantially the way we have been distributing EMBOSS and allows it to be installed on 32 or 64 bit systems. The main changes to be aware of are listed below, in approximate order of importance. > > > > Please feel free to write to the NEBC helpdesk (helpdesk at nebc.nox.ac.uk) if you notice any issues with the new package. > > > > Overview: > > > > bio-linux-emboss is now a wrapper package. It includes the necessary indices for EMBOSS restriction mapping programs, em_pscan for searching prints, patmatmotifs for searching prosite, transcription factor searching using jaspscan, and programs making use of amino acid properties such as pepwindow and pepwindowall. It also includes Jemboss. bio-linux-emboss pulls in the base binaries, documentation and basic data files from Ubuntu packages. The underlying version of EMBOSS on your system is 6.0.1, and should track new versions of EMBOSS as they become available in the Ubuntu repositories. > > > > Major changes: > > > > If you have edited your emboss.default file in the past, it will be kept and saved to /usr/share/EMBOSS/emboss.default.old. You can replace the distributed version /usr/share/EMBOSS/emboss.default with your old version if you wish. The emboss.default file we distribute in bio-linux-emboss supports fetching sequences from the same databases as it has before: embl, emblcds, refseq and uniprot (also aliased as swissprot and trembl). > > > > The pscan and cons programs distributed with the Ubuntu emboss package are called em_pscan and em_cons. This means you will need to call these programs using their new names, and also means that for the moment, these programs are not available through the Jemboss interface. > > > > The EMBASSY versions of Phylips software have changed names. They used to use the same name as native Phylip programs, prefaced by an e (for example, eprotpars runs the EMBASSY version of protpars). Now these programs are prefaced by an f (so, for example, fprotpars). > > > > Not all the software available as EMBASSY packages is yet available as Ubuntu packages. This means that the following software packages are no longer distributed as part of bio-linux-emboss: emnu, esim4, hmmernew, mira, memenew, signature, structure, and topo. Please note that this only refers to the EMBASSY versions of the software. You can still install bio-linux-hmmer and bio-linux-mira to get the native programs. If you are a user of the EMBASSY versions of the software listed in the paragraph and are concerned about losing these programs, please let us know by emailing helpdesk at nebc.nox.ac.uk > > > > The bio-linux-emboss-kmenus package will continue to be available for Bio-Linux 5 systems (based on Ubuntu 8.04). This package provides the graphical interface when Emboss programs are run from the main Bioinformatics menu. This will not work on more recent Ubuntu versions due to an incompatibility with the Kaptain software, and therefore will be removed in Bio-Linux 6. We recommend that people consider using other ways of running the EMBOSS software. For graphical access, we suggest Jemboss, which can be started by typing jemboss on the command line, or by choosing the Jemboss option under the Bioinformatics menu. Another option is to install the web-based package from Ubuntu: emboss-explorer. > > > > regards, > > > > The NEBC Team > > > > > ************************* > NERC Environmental > Bioinformatics Centre > http://nebc.nox.ac.uk > tel: 01491 69 2705 > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > ************************* > > -- > 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. > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > -- > 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. > > -- Bioinformatics Support Unit || http://bsu.ncl.ac.uk/ Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri) Website: http://bsu.ncl.ac.uk/support Twitter: http://twitter.com/nclbsu From obuckley at ceh.ac.uk Mon Mar 8 07:16:40 2010 From: obuckley at ceh.ac.uk (Oliver Buckley) Date: Mon, 08 Mar 2010 12:16:40 +0000 Subject: [Bio-Linux] How to complete installation of new packages Message-ID: <1268050601.7124.9.camel@WLPC882> Dear Bio-Linux Users, The newest version of bio-linux-fastDNAml, bio-linux-mrbayes, bio-linux-njplot, bio-linux-rasmol, bio-linux-tree-puzzle and bio-linux-treeview were released today. Many Bio-Linux systems will pick up this update overnight. In order to complete the installation, you will need to log into your system, and run the command sudo apt-get -f install If your machine does not install updates automatically at night, please update your system and then run the above command from a terminal window. These new packages change substantially the way we have been distributing packages and will allow installation on either 32 or 64 bit systems. Please feel free to write to the NEBC helpdesk (helpdesk at nebc.nox.ac.uk) if you notice any issues with the new package. regards, The NEBC Team ************************* NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk tel: 01491 69 2705 Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB ************************* From a.travis at abdn.ac.uk Mon Mar 8 07:21:56 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Mon, 08 Mar 2010 12:21:56 +0000 Subject: [Bio-Linux] How to complete installation of new packages In-Reply-To: <1268050601.7124.9.camel@WLPC882> References: <1268050601.7124.9.camel@WLPC882> Message-ID: <4B94EBE4.8070800@abdn.ac.uk> Oliver Buckley wrote: > Dear Bio-Linux Users, > > > > The newest version of bio-linux-fastDNAml, bio-linux-mrbayes, > bio-linux-njplot, bio-linux-rasmol, bio-linux-tree-puzzle and > bio-linux-treeview were released today. Many Bio-Linux systems will pick > up this update overnight. In order to complete the installation, you > will need to log into your system, and run the command > > sudo apt-get -f install Hello, Oliver. Debian policy now suggests using "aptitude" instead of "apt-get", because aptitude is more robust. I use: sudo aptitude -f install Can I test installation of Bio-Linux deb's under 64-bit Ubuntu 8.04? Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From obuckley at ceh.ac.uk Mon Mar 8 09:02:36 2010 From: obuckley at ceh.ac.uk (Oliver Buckley) Date: Mon, 08 Mar 2010 14:02:36 +0000 Subject: [Bio-Linux] How to complete installation of new packages In-Reply-To: <4B94EBE4.8070800@abdn.ac.uk> References: <1268050601.7124.9.camel@WLPC882> <4B94EBE4.8070800@abdn.ac.uk> Message-ID: <1268056956.7124.17.camel@WLPC882> The packages that we currently have as 64-bit are already available through our package repository and everyone is more than welcome to try them out. We are targeting the packages at the new LTS (10.04) so it is possible that there could be some compatibility issues with 8.04. If there is any further discussion about our 64-bit packages please use the bio-linux-dev mailing list. Also if there are any issues with the 64-bit packages please let us know through the helpdesk or the bio-linux-dev list. Thanks Oliver On Mon, 2010-03-08 at 12:21 +0000, Tony Travis wrote: > Oliver Buckley wrote: > > Dear Bio-Linux Users, > > > > > > > > The newest version of bio-linux-fastDNAml, bio-linux-mrbayes, > > bio-linux-njplot, bio-linux-rasmol, bio-linux-tree-puzzle and > > bio-linux-treeview were released today. Many Bio-Linux systems will pick > > up this update overnight. In order to complete the installation, you > > will need to log into your system, and run the command > > > > sudo apt-get -f install > > Hello, Oliver. > > Debian policy now suggests using "aptitude" instead of "apt-get", > because aptitude is more robust. I use: > > sudo aptitude -f install > > Can I test installation of Bio-Linux deb's under 64-bit Ubuntu 8.04? > > Bye, > > Tony. -- ******************************************** Dr. Oliver Buckley Bioinformatician NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk Tel: (01491) 69 2705 Centre for Ecology and Hydrology Maclean Building Wallingford, OX10 8BB ********************************************