From dswan at ceh.ac.uk Fri Apr 16 05:38:31 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Fri, 16 Apr 2004 10:38:31 +0100 Subject: [Bio-Linux] Red Hat Linux 9.0 EOL (End of Life) Message-ID: <407FA997.7010104@ceh.ac.uk> Dear All, As some of you may be aware Red Hat withdraws support for Red Hat Linux 9.0 (the base OS of Bio-Linux) on April 30th 2004. This has left a question of how Bio-Linux machines will be updated with security updates, bug fixes etc. after this date and before the release of Bio-Linux 4.0 in October. To reassure everyone that their machines will not suddenly go out of date, when the EOL occurs I will be sending out an update over the list. This update will replace your /etc/yum.conf file (Yum is the system that updates your machines). The yum.conf will point to the "Fedora Legacy Project", which is going to support Red Hat 9.0 for security and bugfixes for at least 1.5 years. For more information on the Fedora Legacy Project please see their website at: http://www.fedoralegacy.org/ Please note that if you are still on Bio-Linux 2.0 or 2.1 as a researcher outside the NERC EG community you are not currently getting security updates, and if you have no plans to upgrade to Bio-Linux 3.0 then you might wish to install Yum and use the Fedora Legacy Project to keep your machines up to date. If you are interested in learning how to do this please get in touch. Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From btiwari at ceh.ac.uk Wed Apr 21 04:35:11 2004 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 21 Apr 2004 09:35:11 +0100 Subject: [Bio-Linux] new package for Bio-Linux perhaps? Mesquite Message-ID: Hello, An evolutionary ecologist friend of mine suggested the Mesquite package for inclusion with future releases of Bio-Linux. Does anyone on this list have any comments about this package, or experience using it that they'd like to share? Dan - what do you think? Bela ************************* Dr. Bela Tiwari Lead Bioinformatician CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* From TSC at bas.ac.uk Wed Apr 21 07:13:31 2004 From: TSC at bas.ac.uk (Thomas Schlitt) Date: Wed, 21 Apr 2004 12:13:31 +0100 Subject: [Bio-Linux] phylip>>protpars bug Message-ID: Dear all I am a new Biolinux user, therefore I am sorry if this email is not sent to the correct mailling list- There is a typo in the /usr/software/exec directory the link "prtopars" should be renamed "protpars"- it links to the correct program Cheers Thomas -------------------------------------------------------------------------- Thomas Schlitt Bioinformatics Research Fellow British Antarctic Survey High Cross, Madingley Road Cambridge CB3 0ET, UK Tel. 0044 1223 221656 From dswan at ceh.ac.uk Wed Apr 21 10:18:20 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 21 Apr 2004 15:18:20 +0100 Subject: [Bio-Linux] Bio-Linux updates Message-ID: <408682AC.50901@ceh.ac.uk> Hi All, We have taken an updated image this week - for those of you who wish to sync your systems against it the image name is: bio-linux_3.0_650_NVIDIA_19042004 There are a number of updates on this image: (o)R (the statistical programming language) has been updated to version 1.9.0. (o)Bioconductor (microarray analysis package running under R) has been updated to version 1.3 (o)We have also fixed the broken protpars link in /usr/software/exec A major tweak to EMBOSS now allows you to retrieve sequences from remote databases, for more information on how to fix this on your own Bio-Linux machine see the following links: http://envgen.nox.ac.uk/envgen/software/archives/000451.html You will need to download this file: http://envgen.nox.ac.uk/envgen/software/archives/emboss.default (o)The latest version of maxdload2 is included in the new image - the MIAME compliant database for maxd, the transcriptomics package. (o)If you wish to check your yum logs recent updates inclde: cvs 1.11.2-17.i386 ethereal 0.10.3-0.90.1.i386 ethereal-gnome 0.10.3-0.90.1.i386 (o)Newly installed on the image by Yum: tkinter 2.2.2-26.i386 tix 1:8.1.4-88.i386 itcl 3.2-88.i386 If you are a subscriber to the trade magazine "The Scientist" then Bio-Linux has a mention this month in their Open Source Software section: http://www.the-scientist.com/yr2004/apr/tech_040412.html For those of you who don't subscribe (and don't wish to sign up on the website) I have included the text below (complete with factual inaccuracies). I did try and help the journalist out with clearly worded replies to his email enquiries, but he still managed to get his wires crossed. Anyone who has dealt with journalists before will not be entirely surprised by this ;) *** Software Watch | Bioinformatics for the Linux-Curious If you've been intrigued by Linux but want to avoid the hassle of repartitioning your hard drive, Bioknoppix (bioknoppix.hpcf.upr.edu) may be just what you need. A bioinformatics-themed version of Knoppix, Bioknoppix, unlike most Linux distributions, does not install to the hard drive; instead it runs from a CD. As a result, the existing operating system is untouched, says Bioknoppix codeveloper Humberto Ortiz of the University of Puerto Rico. "You just pop the CD in and reboot the computer, and up comes Bioknoppix and you do your sequence analysis or whatever," says Ortiz. "Then you pop the CD out and reboot the computer again," to restore the system. That makes Bioknoppix (currently at version 0.2.1 beta) ideal for students, demos, and workshops, he says. Users can save their work to a floppy disk, zip disk, or a USB pen. A full-featured Linux variant, Bioknoppix includes such popular titles as the KDE graphical user interface and the Open Office productivity suite, plus network and programming tools. But it also comes bundled with such open-source bioinformatics tools as EMBOSS, ImageJ, ClustalX, and bioperl. Other applications will be forthcoming, says Ortiz, provided they are both open-source and distributable. The Bioknoppix download is a hefty 688-MB .iso file ready to be burned to disk. At the moment, the team does not provide the software on CD, but Ortiz says they may arrange for a vendor to provide that service for a nominal fee. PENGUIN PUSH But bioknoppix is not the only Knoppix-based Linux distribution customized for bioinformaticians. Late in march, Pratul K. Agarwal of the Oak Ridge National Laboratory released a beta version (0.1) of Vigyaan cd. Described on its website (www.vigyaancd.org) as "an electronic workbench for computational biology and computational chemistry," VigyaanCD (Vigyaan is Hindi for science and knowledge) supplements life science tools with chemical ones like XDrawChem and Ghemical. Another Knoppix distribution is expected this fall. The current version of Bio-Linux (3.0), available from the UK's national environment research council's environmental genomics thematic Programme Data Centre, Oxford University, sports a long list of bundled biological software. But it also requires a very specific computer configuration: a Dell Precision 650, dual 2.4-GHz Xeon CPU workstation with 1 GB RAM, 160 GB hard disk, and a 17-inch flat-panel display. That's because 3.0 is not a true distribution; it is a snapshot, or image, of the installation on just such a computer. As a result, according to the Bio-Linux website (envgen.nox.ac.uk/biolinux.html), "installing it on hardware that is different to ours may cause some initial teething problems." Bio-Linux developer Dan Swan says Bio-Linux 4.0, expected in October, will be Knoppix-based to eliminate this issue. ** regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Wed Apr 21 11:40:04 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 21 Apr 2004 16:40:04 +0100 Subject: [Bio-Linux] new package for Bio-Linux perhaps? Mesquite In-Reply-To: References: Message-ID: <408695D4.6030100@ceh.ac.uk> Bela Tiwari wrote: > Hello, > > An evolutionary ecologist friend of mine suggested the Mesquite > package > for inclusion with future releases of Bio-Linux. > > Does anyone on this list have any comments about this package, or > experience using it that they'd like to share? > > Dan - what do you think? I've just installed it and it seems to run fine. I'm quite happy to include it in the next image update. It *seems* very powerful from my uninformed eye and I haven't made it crash (yet) although I'm not having huge success with the "help" system at the moment. other comments from the more evolutionarily inclined? regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Wed Apr 28 11:58:06 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 28 Apr 2004 16:58:06 +0100 Subject: [Bio-Linux] Problems relating to /var reaching 100% full Message-ID: <408FD48E.9040406@ceh.ac.uk> Dear Bio-Linux admins, A few reports are trickling in with regards to problems which seem wide ranging but may actually be due to full disks on the machine. The Yum system which keeps your machines up to date seems to be filling /var to 100% capacity. You can verify this with : df -m | grep var If you see 100% reported in this line, you need to remove the packages yum has cached with this line. Please type it exactly as rm -rf is very destructive when mistpyed: sudo rm -rf /var/cache/yum/updates/packages/* This will reduce useage to around 20% in var, and may fix sporadic or hard to trace errors you may be experiencing. regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Wed Apr 28 12:15:23 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 28 Apr 2004 17:15:23 +0100 Subject: [Bio-Linux] Problems relating to /var reaching 100% full Message-ID: <408FD89B.6090607@ceh.ac.uk> Chris Beck from Concordia University suggests that a better way to clean out the Yum packages is : sudo yum clean packages - I will add a cron job to the Bio-Linux image in order that this is done on a regular basis. cheers Chris! Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Thu Apr 29 09:36:38 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Thu, 29 Apr 2004 14:36:38 +0100 Subject: [Bio-Linux] New image released for Bio-Linux 3.0 Message-ID: <409104E6.8060900@ceh.ac.uk> Dear all, due to a number of bugfixes we have taken a new image of Bio-Linux. Feel free to sync against the image: bio-linux_3.0_650_NVIDIA_29042004 We have added a script to /etc/cron.monthly to keep the yum cache cleared out. If you wish to add something similar: create a file in /etc/cron.mounthly with the filename yum_clean.sh. Paste in the next 2 lines: #!/bin/sh /usr/bin/yum clean packages then sudo chmod 755 /etc/cron.monthly/yum_clean.sh We have also added the Mesquite package (http://mesquiteproject.org/mesquite/mesquite.html) to the system. We have corrected a symlink in /usr/software/exec - the file "baselmg" should be called "basemlg". We have reorganised /usr/software/documentation as part of our ongoing effort to improve this area of Bio-Linux. We hope to release a complete documentation update soon with all bioinformatics related documentation available and searchable from a single web interface. This requires categorisation of all the software, and the development of a basic content management system for the documentation, some format conversion and a lot of discussion and we currently have a new member of staff (Tanya) dedicated to this effort. As you're no doubt aware, Red Hat 9.0 support runs out tomorrow (April 30th) as soon as I have a replacement yum.conf file ready for distribution I will release it on the list. regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Thu Apr 29 10:27:53 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Thu, 29 Apr 2004 15:27:53 +0100 Subject: [Bio-Linux] Interruption of EGTDC services Message-ID: <409110E9.6090209@ceh.ac.uk> Dear All, First may I just apologise for cross-posting to 3 lists, I understand that this will be annoying for users subscribed to all 3. We are currently migrating our web based services - the website, helpdesk system and mailing lists from our venerable old server to a new high spec machine. In order to do some testing of the new server we plan to take the current machine down over the weekend of 8th and 9th of May. Between 5pm Friday 7th May and 9am Monday 10th May there will be no guaranteed service from the helpdesk, mailing lists or website. If the handover between machines is successful then the new machine will be left in place. If it is clear more work needs to be done, the the old machine will be restored, until such time as the problems with the new server are resolved. If you have developer access to the website please do not make any commits to the site after Thursday 6th May, as I need to freeze the status of the site in order to port it over. I will post another reminder announcement closer to the time. regards. Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk