From dswan at ceh.ac.uk Wed May 5 04:57:20 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 05 May 2004 09:57:20 +0100 Subject: [Bio-Linux] IMPORTANT *Bio-Linux updated yum.conf file* Message-ID: <4098AC70.9000704@ceh.ac.uk> Dear All, FedoraLegacy has finally picked up and started support for Red Hat 9.0. This support will last long after Bio-Linux 4.0 is released, so you can use the systems with confidence. However you do need to edit the yum.conf file on your machines. PLEASE NOTE THIS ALERT IS NOT RELEVANT FOR USERS OF BIO-LINUX 2.X - YOU ARE ADVISED TO CONTACT US FOR AN IMMEDIATE UPGRADE TO 3.0 /etc/yum.conf lists repositories used for Yum updates. To replace it do the following steps. 1) Log in as manager 2) sudo mv /etc/yum.conf /etc/yum.conf.bak 3) sudo vim /etc/yum.conf | sudo pico -w /etc/yum.conf | sudo nedit /etc/yum.conf (One of these, or just use your favourite editor) 4) Paste this into the new file: [main] cachedir=/var/cache/yum debuglevel=2 logfile=/var/log/yum.log pkgpolicy=newest distroverpkg=redhat-release tolerant=1 exactarch=1 [base] name=Red Hat Linux $releasever base baseurl=http://download.fedoralegacy.org/redhat/$releasever/os/$basearch [updates] name=Red Hat Linux $releasever updates baseurl=http://download.fedoralegacy.org/redhat/$releasever/updates/$basearch [legacy-utils] name=Fedora Legacy utilities for Red Hat Linux $releasever baseurl=http://download.fedoralegacy.org/redhat/$releasever/legacy-utils/$basearch 5) Save the file 6) Test the file : sudo yum update you should see something like this: Gathering header information file(s) from server(s) Server: Red Hat Linux 9 base Server: Fedora Legacy utilities for Red Hat Linux 9 Server: Red Hat Linux 9 updates Finding updated packages Downloading needed headers No Packages Available for Update No actions to take If it does an update, so much the better :) If you see any errors or these instructions are not clear to you please contact me off 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 Wed May 5 11:50:10 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 05 May 2004 16:50:10 +0100 Subject: [Bio-Linux] envgen server downtime Message-ID: <40990D32.1030305@ceh.ac.uk> Apologies once again for the cross-posting In order to test the replacement envgen.nox.ac.uk server I will be taking envgen.nox.ac.uk offline and installing the new server. This is a preliminary stage to the migration to allow us (hopefully) to have the new server in place over the weekend. All services (mailing lists, helpdesk, website) will be effectively missing between 8.30am and 9.30am tomorrow morning. Any email recieved to the mailing lists, or helpdesk will not NOT be honoured or relayed. If email goes AWOL in that hour, I apologise in advance, but please bear with us as these short outages will enable us to deliver a reliable service in the future. 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 Fri May 7 05:23:37 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Fri, 07 May 2004 10:23:37 +0100 Subject: [Bio-Linux] Web proxies and Yum Message-ID: <409B5599.8070402@ceh.ac.uk> Hi All, It has been pointed out recently that if your instituion has a web proxy for outgoing web traffic then your Yum updates might not be running. If you have a web-proxy then it is most likely you will have had to set this in Mozilla's preferences, or in your GeneSpring preferences in some cases. Yum has no configuration option for proxy servers, and as it works on the same ports as your web browser will not work if you require a proxy set. In order to force Yum to use a proxy take the following steps: First you need to know what your proxy server is, and which port it is running on. In this example we will use: http://proxy.someuni.ac.uk:8080/ as our "pretend proxy" You will need to find your own proxy setting. 8080 is a common proxy port. This will need to be set up in /usr/software/bioenvrc 1) Log in as manager 2) Edit /usr/software/bioenvrc with your favourite text editor 3) add this line somewhere: export http_proxy=http://proxy.someuni.ac.uk:8080/ 4) Save the file, log out, log in as manager 5) sudo yum update Thanks to Hazel for bringing this issue to our attention. 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 Fri May 7 10:23:18 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Fri, 07 May 2004 15:23:18 +0100 Subject: [Bio-Linux] envgen.nox.ac.uk downtime Message-ID: <409B9BD6.7020707@ceh.ac.uk> Final reminder! The envgen.nox.ac.uk system will be out of action from 5pm today. Please do not mail helpdesk requests or mailing list items if you wish them to be replied to! Normal service will resume Monday morning after work on the weekend on the replacement server. The website will most likely be intermittently available in some form over the weekend. regards and sorry for the inconvenienve, 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 May 19 11:12:03 2004 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 19 May 2004 16:12:03 +0100 Subject: [Bio-Linux] problem with arb setup on some machines Message-ID: Hello We have recently received reports about problems with the current setup of Arb on some machines. Whether or not your Bio-Linux installation has this problem depends on if you upgraded vs. installed, when you upgraded or installed, etc, etc. So if you believe you or anyone associated with your machine, will ever use Arb, please can you check and correct the following: Please see if you have a directory called /home/db/pt_server If not, as manager, go into /home/db and create a directory called pt_server: sudo mkdir /home/db/pt_server You will then need to change the permissions on that directory so that the user you want to be be able to alter things in this directory has permission to do so. If that is always going to be manager, then change the ownership to manager for example. We have also noticed there are two broken links in /usr/software/arb/arb/lib. Fixing them may or may not affect anything, but if you want to fix them, move into /usr/software/arb/arb/lib and 1) remove the current link to ghostscript and make the link: sudo ln -s /usr/bin/ghostscript ghostscript 2) copy the Xlib directory from an older arb installation into /usr/software/arb/arb: sudo cp -R /usr/software/arb/arb_15.6.02/Xlib /usr/software/arb/arb Please let us know if you have come across any other problems on Bio-Linux. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* From keith.jolley at medawar.oxford.ac.uk Thu May 20 05:49:41 2004 From: keith.jolley at medawar.oxford.ac.uk (Keith Jolley) Date: Thu, 20 May 2004 10:49:41 +0100 Subject: [Bio-Linux] Mozilla version downgraded Message-ID: I noticed this morning that the version of mozilla I was using had reverted to version 1.4 (this was apparent because closing it in version 1.5 with multiple tabs open prompts you if you really want to close all open tabs, version 1.4 doesn't). Looking in /usr/bin showed that there was a mozilla executable present rather than a symlink to the most recent version. I restored it to the way it was by doing: sudo rm /usr/bin/mozilla sudo ln -s /usr/local/mozilla/mozilla mozilla and everything is fine again. Not sure why this happened! Keith -- Dr. Keith Jolley The Peter Medawar Building for Pathogen Research University of Oxford South Parks Road Oxford, OX1 3SY From tbooth at ceh.ac.uk Thu May 27 10:05:50 2004 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 May 2004 15:05:50 +0100 Subject: [Bio-Linux] Recording CDs on Bio-Linux 3 Message-ID: <1085666750.6240.387.camel@ivpcp044.nerc-oxford.ac.uk> Dear Bio-Linux users, Following some recent questions and suggestions, we have updated and clarified the FAQ information regarding using the CD writer provided on the Bio-Linux machines. In particular, these instructions suggest a piece of software, gcombust, which we find particularly effective. They also address issues with users being prompted for a root password to access the CD recording features. You might also want to try out the xcdroast and gtoaster programs not mentioned in the FAQ. To run either of these, you will need to be in the manager account - if you have problems with the desktop icons you can run them directly from the command line as follows: sudo /usr/sbin/xcdroast and sudo /usr/bin/gtoaster-root respectively. Let us know if you have any comments - we want to make CD burning as easy as possible in Bio-Linux 4! Regards, Tim Booth - EGTDC ------------------ The new user FAQ entry in full: (see http://envgen.nox.ac.uk/envgen/software/archives/000413.html) 13 - How do I make use of the CD writer? The default setup is that only the manager may use the CD writer. Read on for how to change this. Firstly, if you want to use the CD writer for backup purposes, it is strongly recommended to make an archive of your files, and to burn this file to a CD. Here's a suitable command to produce a compressed archive holding 2 directories: tar czvf archive_name.tar.gz directory1 directory2 The letters czvf mean create a zipped file, with verbose output, with the filename "archive.tar.gz". You may also find the File Roller program from the Accessories menu useful, as this provides a graphical interface. RedHat provides several CD recording programs, each with various strengths and weaknesses. We suggest using 'gcombust'. First put all the files you want to write to the CD into a single directory or archive file. Then insert a blank CD, and start the program from the command line by typing: sudo gcombust & Click on the "data files" tab. By clicking on the "add directory" button you can add the directory containing your files to the list of files to be backed up. When you have finished adding directories, click "cancel" to close the file browser window. Clicking on "compute estimate" will calculate the total size of the files you are about to burn to CD. Next, click on the "burn" tab. Select the appropriate speed for your CD burner (32 works well on the Precision 650s), and make sure that "dummy test run" is not ticked. Then, click on "detect SCSI drive" and "check SCSI settings". Finally, click the "burn" button and prepare for a long wait. When finished, a box with the message "operation completed successfully" will appear. To allow all users to create CDs, a simple command needs to be run by the manager: sudo chmod 4755 /usr/bin/cdrecord This will take permanent effect; all users may now run the gcombust command without the use of 'sudo'. You may want to create an icon for gcombust on your desktop or pull-down menu, by right clicking and selecting to make a New Launcher. Technical Note: The above command uses the 'setuid' feature so that the cdrecord process will run as root. The gcombust documentation notes that this is a potential security risk for shared machines. If you have any concerns, please contact the helpdesk for advice. * From btiwari at ceh.ac.uk Fri May 28 11:18:45 2004 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri, 28 May 2004 16:18:45 +0100 Subject: [Bio-Linux] For people running GeneSpring on Bio-Linux machines Message-ID: Hello It has come to our attention that the current updates to GeneSpring contain a file called GeneSpring.lax with a line reading: lax.nl.java.option.java.heap.size.max= This line should in fact contain a number such as: lax.nl.java.option.java.heap.size.max=1000000000 You or your users may not have noticed an issue with this yet, but when the genomes they are trying to load hit a big enough size, they will! The error resulting shows itself as a box labelled "Out of Memory" and a message saying "Sorry, you have run out of memory. Please contact Technical Support for help with this problem." We have contacted Silicon Genetics about this problem, so the solutions are to: 1) wait until Silicon Genetics puts out an updated GeneSpring.lax file and put this in your /home/db/SiliconGenetics/GeneSpring/data folder. or 2) Edit the GeneSpring.lax file and add a number like that shown in the line above. There is some info about errors related to the GeneSpring.lax file on the Silicon Genetics website at: http://www.silicongenetics.com/cgi/TNgen.cgi/GeneSpring/GSnotes/Notes/dll_fatal_error and we have requested that they add information specific to the problems currently being seen. thanks Bela Tiwari ************************* Dr. Bela Tiwari Lead Bioinformatician CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 *************************