Hi all, I'm new to Centos, just moved here from Gentoo Linux. I have to install a server for bioinformatics purposes and I see that default yum repositories do not include any bioinformatics software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't find a valuable solution: which is (or which are) the best repository I should add to have a satisfying list of bioinfo rpm? Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.centos.org/pipermail/centos/attachments/20081125/f3f32551/attachment-0003.html>
Davide Cittaro <> scribbled on Tuesday, November 25, 2008 10:13 AM:> I'm googling a bit but I can't find a > valuable solution: which is (or which are) the best repository I should add > to have a satisfying list of bioinfo rpm?You could try rpmforge. I add and enable this repo routinely. I find it rather good generally speaking. FWIW, I haven't heard of any repos with specifically bioinfo rpms. -- /Sorin -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 5126 bytes Desc: not available URL: <http://lists.centos.org/pipermail/centos/attachments/20081125/d462a3fc/attachment-0003.bin>
On Nov 25, 2008, at 10:46 AM, Sorin Srbu wrote:> > You could try rpmforge. I add and enable this repo routinely. I find > it rather > good generally speaking. FWIW, I haven't heard of any repos with > specifically > bioinfo rpms.I've added it but I cannot find bioinfo packages... I've seen people adding this repo.bioinformatics.upenn.edu and others but they seem to be seldom updated... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */
> -----Original Message----- > From: centos-bounces at centos.org > [mailto:centos-bounces at centos.org] On Behalf Of Davide Cittaro > Sent: Tuesday, November 25, 2008 4:13 AM > To: centos at centos.org > Subject: [CentOS] bioinformatics repository? > > Hi all, I'm new to Centos, just moved here from Gentoo Linux. > I have to install a server for bioinformatics purposes and I > see that default yum repositories do not include any > bioinformatics software (i.e. ncbi-toolkit, blat, and > others). I'm googling a bit but I can't find a valuable > solution: which is (or which are) the best repository I > should add to have a satisfying list of bioinfo rpm?David, you could try Checking out the Scientific Linux Project to Maybe add and use there Repos. It should also be binary compatable with CentOS. That would be the only Distributon that I know of that would maybe have what you need. The only others would be maybe Debian Based Systems because of the huge alternate package options. But off course then you would need to convert the debian packages to rpm format and there is also a tool to do that. JohnStanley
Davide Cittaro wrote:> Hi all, I'm new to Centos, just moved here from Gentoo > Linux. > I have to install a server for bioinformatics purposes and > I see that default yum repositories do not include any > bioinformatics software (i.e. ncbi-toolkit, blat, and > others). I'm googling a bit but I can't find a > valuable solution: which is (or which are) the best > repository I should add to have a satisfying list of bioinfo > rpm?These look like BioRpms to me BioRPMS :- Bioinformatics RPMs Repository http://informatics.umdnj.edu/BioRPMs/ Regards, Vandaman.
Davide Cittaro wrote:> Hi all, I'm new to Centos, just moved here from Gentoo Linux. > I have to install a server for bioinformatics purposes and I see that > default yum repositories do not include any bioinformatics software > (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't > find a valuable solution: which is (or which are) the best repository I > should add to have a satisfying list of bioinfo rpm? > > Thanks > > d > > > /* > Davide Cittaro > > Cogentech - Consortium for Genomic Technologies > via adamello, 16 > 20139 Milano > Italy >Hi Maybe you can find in EPEL repository. http://fedoraproject.org/wiki/EPEL regards Marcelo
On Nov 25, 2008, at 4:12 AM, Davide Cittaro wrote:> Hi all, I'm new to Centos, just moved here from Gentoo Linux. > I have to install a server for bioinformatics purposes and I see > that default yum repositories do not include any bioinformatics > software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit > but I can't find a valuable solution: which is (or which are) the > best repository I should add to have a satisfying list of bioinfo rpm? > > Thanks > > d > > > /* > Davide Cittaro >Some of these packages (perl-bioperl, python-biopython, wise2) can also be found in Fedora. I have usually been able to rebuild the src rpms for CentOS without difficulty. Rpmforge has most of the perl packages required. Tony Schreiner