From jaa53 at cornell.edu Tue Jul 11 18:03:19 2006 From: jaa53 at cornell.edu (Jose Andres) Date: Tue, 11 Jul 2006 18:03:19 -0400 Subject: [Bio-Linux] OmegaMap on bio-linux? In-Reply-To: References: Message-ID: Hi all, Daniel Wilson has recently put out a software package to estimate diversifying selection in the presence of recombination using the the ratio of non-synonymous to synonymous polymorphism (see Wilson and McVean 2006, Genetics 172: 1411-1425). I am most interested in using this software in a Bio-linux machine and I was wondering if someone has already done it. Daniel's web page only supports the Windows XP exacutable, but the source code is also available (http:// www.danielwilson.me.uk/frame.html?http://www.danielwilson.me.uk/ publications.html). I can always compile the program using make, but I am not sure how I should install the program [sorry I am still at the steep part of my (bio)linux learning curve]. Any suggestions? Has anyone use OmegaMap on a Bio-linux machine? Another possibility (assuming there is a critical mass of Bio-linux users interested in this package) is to develop a Bio-linux version based the source code already available. I do not if this is possible or how difficult it might be, but it is probably worth trying (my apologies for not been able to do it myself). Thanks, /Jose -------------------------------------------------------------- Jose A. Andres, PhD Dpt. Ecology and Evolutionary Biology Cornell University. 14850 Ithaca, NY, USA From btiwari at ceh.ac.uk Wed Jul 12 07:29:45 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 12 Jul 2006 12:29:45 +0100 Subject: [Bio-Linux] OmegaMap on bio-linux? Message-ID: Hi Jose, Thanks for your email about OmegaMap. >I can always compile the program using make Have you tried this yet? If so, diid it work? If so, then we could probably make a Bio-Linux package out of it. Otherwise it will depend on how easy it is to get this to compile on Bio-Linux. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* From bioinformatics.lists at gmail.com Wed Jul 12 10:59:48 2006 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Wed, 12 Jul 2006 15:59:48 +0100 Subject: [Bio-Linux] OmegaMap on bio-linux? In-Reply-To: References: Message-ID: On 7/12/06, Bela Tiwari wrote: > Hi Jose, > > Thanks for your email about OmegaMap. > > >I can always compile the program using make > > Have you tried this yet? If so, diid it work? If so, then we could probably make a Bio-Linux package out of it. > > Otherwise it will depend on how easy it is to get this to compile on Bio-Linux. It compiles cleanly on OS X 10.4 with gcc 4 and Bio-Linux 4 with gcc 3.3 to produce 5 or 6 small binaries so there shouldn't be any problem! cheers, Dan -- Senior Research Associate, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26) Website: http://bioinf.ncl.ac.uk/support/ From S.Paterson at liverpool.ac.uk Wed Jul 12 11:25:37 2006 From: S.Paterson at liverpool.ac.uk (Steve Paterson) Date: Wed, 12 Jul 2006 16:25:37 +0100 Subject: [Bio-Linux] OmegaMap on bio-linux? In-Reply-To: References: Message-ID: <1D56B2F5-8024-42D5-AADF-4E4132B7A73A@liv.ac.uk> Bela, Re. OmegaMap. This would be a great addition to Bio-Linux to sit alongside PAML. It would also be very useful for my NERC-PGP project so I for one would be keen to see it in forthcoming distributions of Bio-Linux. Thanks also to Jose for spotting this. Steve On 11 Jul 2006, at 23:03, Jose Andres wrote: > Hi all, > > Daniel Wilson has recently put out a software package to estimate > diversifying selection in the presence of recombination using the > the ratio of non-synonymous to synonymous polymorphism (see Wilson > and McVean 2006, Genetics 172: 1411-1425). I am most interested in > using this software in a Bio-linux machine and I was wondering if > someone has already done it. Daniel's web page only supports the > Windows XP exacutable, but the source code is also available > (http://www.danielwilson.me.uk/frame.html?http:// > www.danielwilson.me.uk/publications.html). > > I can always compile the program using make, but I am not sure how > I should install the program [sorry I am still at the steep part > of my (bio)linux learning curve]. > Any suggestions? Has anyone use OmegaMap on a Bio-linux machine? > > Another possibility (assuming there is a critical mass of Bio- > linux users interested in this package) is to develop a Bio-linux > version based the source code already available. I do not if this > is possible or how difficult it might be, but it is probably worth > trying (my apologies for not been able to do it myself). > > Thanks, > > /Jose > > > -------------------------------------------------------------- > Jose A. Andres, PhD > Dpt. Ecology and Evolutionary Biology > Cornell University. 14850 Ithaca, NY, USA > > > _______________________________________________ > Bio-linux mailing list > Bio-linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux ============= Dr. Steve Paterson Lecturer in host-parasite biology School of Biological Sciences University of Liverpool LIVERPOOL, UK L69 7ZB Tel. 0151 795 4521 Fax. 0151 795 4408 email s.paterson at liv.ac.uk Rm. 202 Biosciences Building http://pcwww.liv.ac.uk/~stevep11/PatHome.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaa53 at cornell.edu Wed Jul 12 12:02:50 2006 From: jaa53 at cornell.edu (Jose A. Andres) Date: Wed, 12 Jul 2006 12:02:50 -0400 (EDT) Subject: [Bio-Linux] OmegaMap on bio-linux? In-Reply-To: References: Message-ID: <54619.132.236.111.235.1152720170.squirrel@webmail.cornell.edu> Hi, I 've tried to compiled it myself but get the following error: make: *** No rule to make target `DNA.h', needed by `likelihood.o'. Stop. Any suggestions? I've checked /usr/bin/ of my bio-linux and runs gcc3.3 (Dan got it to work so I am obviously doing something wrong) I also had problems trying to compile it on my Mac OSX (also running gcc3.3) Thanks, /Jose From bioinformatics.lists at gmail.com Thu Jul 13 07:27:24 2006 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Thu, 13 Jul 2006 12:27:24 +0100 Subject: [Bio-Linux] OmegaMap on bio-linux? In-Reply-To: <54619.132.236.111.235.1152720170.squirrel@webmail.cornell.edu> References: <54619.132.236.111.235.1152720170.squirrel@webmail.cornell.edu> Message-ID: On 7/12/06, Jose A. Andres wrote: > > Hi, > I 've tried to compiled it myself but get the following error: > > make: *** No rule to make target `DNA.h', needed by `likelihood.o'. Stop. > > Any suggestions? I've checked /usr/bin/ of my bio-linux and runs gcc3.3 > (Dan got it to work so I am obviously doing something wrong) > > I also had problems trying to compile it on my Mac OSX (also running gcc3.3) Hi Jose, I have sent Bela the Linux binaries I generated; would you be interested in my sending you the OS X ones as well? I can test them on 10.3.9 as well if you like.. Dan -- Senior Research Associate, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26) Website: http://bioinf.ncl.ac.uk/support/ From JK at novozymes.com Thu Jul 27 07:10:49 2006 From: JK at novozymes.com (JK (Jesper Agerbo Krogh)) Date: Thu, 27 Jul 2006 13:10:49 +0200 Subject: [Bio-Linux] Debian source packages? Message-ID: <934F95E71B6C9347A873C42AE3C196190FFF5A7B@NZT0004E.dknz.nzcorp.net> Hi. We currently using Ubuntu on both amd64 and i386 as platform for our Biocomputing needs. We're reasonably skilled in packaging(and compiling) Debian packages. So in order to get the Biolinux packages on the platforms I would like to know if The Debian source-packages are available somewhere. I've been looking a bit at the Web-archive, but they don't seem to be included in the Debian repository. Thanks. -- Jesper Krogh, Novozymes A/S From ajt at rri.sari.ac.uk Thu Jul 27 10:36:53 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Thu, 27 Jul 2006 15:36:53 +0100 Subject: [Bio-Linux] Debian source packages? In-Reply-To: <934F95E71B6C9347A873C42AE3C196190FFF5A7B@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190FFF5A7B@NZT0004E.dknz.nzcorp.net> Message-ID: <44C8CF85.5010602@rri.sari.ac.uk> JK (Jesper Agerbo Krogh) wrote: > Hi. > > We currently using Ubuntu on both amd64 and i386 as platform for our > Biocomputing needs. We're reasonably skilled in packaging(and compiling) > Debian packages. > > So in order to get the Biolinux packages on the platforms I would like > to know if > The Debian source-packages are available somewhere. I've been looking a > bit at the > Web-archive, but they don't seem to be included in the Debian > repository. Hello, Jesper. We are developing 'biobuntu', which consists of i386 Bio-Linux4 packages installed with other freely available bioinformatics software under i386 Ubuntu 'Dapper' 6.06 LTS, for our NBX (NuGO Black Box) project: http://nbx1.rri.sari.ac.uk I'm interested to hear about your experience of installing/running Bio-Linux packages under Ubuntu. We had to install the "xlibs" package from an earlier version of Ubuntu before I could install the public Bio-Linux4 packages from NEBC. I am also interested in an amd64 version of Bio-Linux. The source code is already present in most of the 'binary' Bio-Linux debs. I had thought of breaking out the source and creating deb-src packages, but don't have time on the current project. For now, we are running a 32-bit kernel and 32-bit applications on "Iwill" small form-factor dual Opteron servers: http://www.iwill.net/product_2.asp?p_id=36 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 From jmartins+ at pitt.edu Thu Jul 27 11:04:10 2006 From: jmartins+ at pitt.edu (Jeremy Martinson) Date: Thu, 27 Jul 2006 11:04:10 -0400 Subject: [Bio-Linux] Debian source packages? In-Reply-To: <44C8CF85.5010602@rri.sari.ac.uk> References: <934F95E71B6C9347A873C42AE3C196190FFF5A7B@NZT0004E.dknz.nzcorp.net> <44C8CF85.5010602@rri.sari.ac.uk> Message-ID: <659171280607270804k77d160ebr6cfc3cbbea200f13@mail.gmail.com> I too am running several Bio-Linux packages under Ubuntu Dapper. I had to install xlibs, but apart from that they install perfectly and run very well - I even get automatic updates of the packages I have installed. I would also be interested in a 64-bit version of Bio-Linux. At the moment I have installed regular i386 Ubuntu on my AMD64 PC because it is sometimes too challenging to fool some of the programs that require the i386 environment into running on a 64-bit OS. Jeremy On 7/27/06, Tony Travis wrote: > > JK (Jesper Agerbo Krogh) wrote: > > Hi. > > > > We currently using Ubuntu on both amd64 and i386 as platform for our > > Biocomputing needs. We're reasonably skilled in packaging(and compiling) > > Debian packages. > > > > So in order to get the Biolinux packages on the platforms I would like > > to know if > > The Debian source-packages are available somewhere. I've been looking a > > bit at the > > Web-archive, but they don't seem to be included in the Debian > > repository. > > Hello, Jesper. > > We are developing 'biobuntu', which consists of i386 Bio-Linux4 packages > installed with other freely available bioinformatics software under i386 > Ubuntu 'Dapper' 6.06 LTS, for our NBX (NuGO Black Box) project: > > http://nbx1.rri.sari.ac.uk > > I'm interested to hear about your experience of installing/running > Bio-Linux packages under Ubuntu. We had to install the "xlibs" package > from an earlier version of Ubuntu before I could install the public > Bio-Linux4 packages from NEBC. > > I am also interested in an amd64 version of Bio-Linux. The source code > is already present in most of the 'binary' Bio-Linux debs. I had thought > of breaking out the source and creating deb-src packages, but don't have > time on the current project. For now, we are running a 32-bit kernel and > 32-bit applications on "Iwill" small form-factor dual Opteron servers: > > http://www.iwill.net/product_2.asp?p_id=36 > > 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 > > _______________________________________________ > Bio-linux mailing list > Bio-linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -- Dr Jeremy Martinson Assistant Professor University of Pittsburgh Dept. Infectious Diseases & Microbiology Graduate School of Public Health 130 DeSoto St Pittsburgh, PA 15261 + Tel: 412-624-5646 Fax: 412-383-8926 + email: jmartins at pitt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: