From ajt at rri.sari.ac.uk Sun Sep 10 10:28:23 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Sun, 10 Sep 2006 15:28:23 +0100 Subject: [Bio-Linux] Phylip 'factor' program Message-ID: <45042107.5000101@rri.sari.ac.uk> I've just encountered a name clash with the Phylip 'factor' program, which is installed under Bio-Linux as: /usr/local/bin/factor -> /usr/local/bioinf/phylip/phylip/bin/factor and the 'standard' Linux 'factor' program installed in: /usr/bin/factor Normally, /usr/local/bin precedes /usr/bin in the default PATH, so the Phylip version takes precedence. However, this breaks the 'standard' version and I suggest renaming the Bio-Linux 'factor' - For example: /usr/local/bin/factor.phylip. Alternatively, you could have a 'phylip' command/shell that sets up the correct paths for Phylip and don't install links to the Phylip programs in /usr/local/bin. I do this with Staden for similar reasons(!): --- cut here --- cut here --- #!/bin/sh # @(#)staden.sh 2005-11-29 A.J.Travis # # Set up environment for Staden package # export STADENROOT=/usr/local/staden . $STADENROOT/staden.profile export PS1="[\u@\h \W]\:staden$ " exec /bin/sh --- cut here --- cut here --- Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From a.gossner at ed.ac.uk Mon Sep 11 04:31:07 2006 From: a.gossner at ed.ac.uk (A Gossner) Date: Mon, 11 Sep 2006 09:31:07 +0100 Subject: [Bio-Linux] Disappearing menus Message-ID: <45051ECB.8090501@ed.ac.uk> Hi Does anyone have any ideas about restoring menu items, seems mainly to be scientific packages on the science menus icon that are disappearing, have tried update- menus but no joy though did work on previous disappearances. Anton Gossner -- Dr A Gossner Centre for Infectious Diseases University of Edinburgh Summerhall Square Edinburgh EH9 1QH A.Gossner at ed.ac.uk Tel. no. 0131 6507943 or 6506168 Fax. no 0131 6506511 From et22 at leicester.ac.uk Mon Sep 11 05:27:27 2006 From: et22 at leicester.ac.uk (Tauber, Dr E.) Date: Mon, 11 Sep 2006 10:27:27 +0100 Subject: [Bio-Linux] Linux program for fragment analysis Message-ID: <0F0BFB9DA110794CA64C94D36F6BF5A307556B2F@sumac.cfs.le.ac.uk> Dear all, Is there a Linux program that handles the output files of the AB3100 genetic analyser and produce pherograms for fragment analysis (like the Windows GeneMapper or GeneScan)? Thanks, Eran Eran Tauber (PhD) Lecturer in Molecular Evolution Dept. of Genetics University of Leicester University Rd, Leicester LE1 7RH England ____________________________________________________________ Phone: 44 (0)116 252-3455, 252-3421 (lab) Fax: 44 (0)116 252-3378 www.le.ac.uk/genetics/et22 From btiwari at ceh.ac.uk Mon Sep 11 06:25:33 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Mon, 11 Sep 2006 11:25:33 +0100 Subject: [Bio-Linux] Disappearing menus Message-ID: Hi Anton, I am not sure what the problem is with the menu. Stewart is away this week, but will hopefully get back to you via the helpdesk next week. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* >>> a.gossner at ed.ac.uk 11/09/2006 09:31:07 >>> Hi Does anyone have any ideas about restoring menu items, seems mainly to be scientific packages on the science menus icon that are disappearing, have tried update- menus but no joy though did work on previous disappearances. Anton Gossner -- Dr A Gossner Centre for Infectious Diseases University of Edinburgh Summerhall Square Edinburgh EH9 1QH A.Gossner at ed.ac.uk Tel. no. 0131 6507943 or 6506168 Fax. no 0131 6506511 _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From ajt at rri.sari.ac.uk Mon Sep 11 09:42:22 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Mon, 11 Sep 2006 14:42:22 +0100 Subject: [Bio-Linux] Disappearing menus In-Reply-To: References: Message-ID: <450567BE.8010800@rri.sari.ac.uk> Bela Tiwari wrote: > Hi Anton, > > I am not sure what the problem is with the menu. Stewart is away this week, but will hopefully get back to you via the helpdesk next week. Hello, Bela and Anton. There was a bug in the Ubuntu version of gdm recently that compromised the Debian/Science menu. This is now fixed in Ubuntu, but may still be an issue under Debian. Ubuntu is, broadly speaking, based on Debian Etch and packages from Etch are migrated into Debian Sarge, which forms the basis of Bio-Linux4. The Debian bug report for Etch is here: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=246224 Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ajt at rri.sari.ac.uk Thu Sep 21 08:25:27 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Thu, 21 Sep 2006 13:25:27 +0100 Subject: [Bio-Linux] Re: Bio-Linux In-Reply-To: References: Message-ID: <451284B7.7080308@rri.sari.ac.uk> Casey M. Finnerty, Ph. D. wrote: > Dear Dr. Travis: > > I saw your post below, and I have a question for you. I am also > interested in installing the Bio-Linux packages onto some machines > running (K)ubuntu Dapper Drake. I looked for the xlibs package you > mentioned and found it in the hoary repository. I also found xlibs-dev > in the Dapper repository. Is it possible that the latter would allow > Bio-Linux installation? I hesitate to install the old xlibs, as I worry > that it might mess up other parts of my system. (e.g., I see that xlibs > ?Breezy? was designed to remove all the XKB configuration files in the > xlibs package.) Hello, Casey. I also found xlibs-dev in Dapper, but the bio-linux-base directories depended on xlibs, and xlibs-dev did not satisfy that dependency. In fact the xlibs from Hoary is a transitional package used to satisfy dependencies. It only installs these files: /. /usr /usr/share /usr/share/doc /usr/share/doc/xlibs /usr/share/doc/xlibs/copyright /usr/share/doc/xlibs/changelog.Debian.gz > If you still recommend using xlibs Hoary, please let me know if you?ve > experienced any problems as a result. No, I didn't experience any problems. However, the "xlibs" dependency of bio-linux-base-directories package has now been removed, so I've removed xlibs from my 'biobuntu' system because it's no longer needed. If you want to know more about our 'biobuntu' project, which is part of my NBX (NuGO Black Box) project, please have a look at: http://nbx1.rri.sari.ac.uk We've remastered the Ubuntu Dapper 6.06 LTS 'live' install CD with all the 'public' Bio-Linux packages pre-installed, but it does not yet have anything like the functionality of the NEBC 'live' DVD :-) Our 'biobuntu' DVD is still a work in progress, and is primarily being developed as a way of installing pre-configured 'biobuntu' onto a hard disk. Although this can be done with the Knoppix-based NEBC 'live' DVD, the resulting Linux installation it creates is very difficult to upgrade because of the strange mixture of packages from different distributions used in Knoppix. The 'biobuntu' DVD is also intended to be used as a 'rescue' DVD for the NBX's if they go wrong. > Thanks! > > Casey > > *********************** > Hello, Bio-Linux'ers > > As part of my NuGO 'Black-Box' project, I've been comparing Ubuntu > 'Dapper' and Debian 'Etch': One reason why I hesitated to adopt Ubuntu > 'Dapper', initially, is that the Bio-Linux 'base-directories' package > has a dependency on Debian 'xlibs' which is not present in Ubuntu > 'Dapper'. This package is, however, present in Ubuntu 'Hoary', so I > installed the 'xlibs' package from 'Hoary' into 'Dapper' and Bio-Linux > now installs and runs OK under Ubuntu (with the sun-java packages). > [...] Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687