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@ifom-ieo-campus.it */
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.
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@ifom-ieo-campus.it */
Davide Cittaro wrote on Tue, 25 Nov 2008 11:23:44 +0100:
repo.bioinformatics.upenn.edu
and others but they seem to be seldom updated...
but they may well be your only ressource here, bioinformatics surely isn't a widespread task given the whole userbase ;-) You may want to contact the maintainers of such a repo and ask if they can provide updates more often. I gather that, apart from time constraints etc., they may also need some encouragement as they are not catering too so many users.
Kai
-----Original Message----- From: centos-bounces@centos.org [mailto:centos-bounces@centos.org] On Behalf Of Davide Cittaro Sent: Tuesday, November 25, 2008 4:13 AM To: centos@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
Hello John, and thanks for the tips
On Nov 25, 2008, at 11:59 AM, John wrote:
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.
Unfortunately that repos is suitable for physics and not really for biology... :-( I found some useful rpm in FC6 repository but still I miss a lot of packages. What is strange is that lot of those packages are standard on less spread OS (I use Gentoo and FreeBSD)...
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.
That's interesting... is it a yum wrapper for apt-get or do I have to download .deb packages and resolve dependencies on my own?
Thanks again
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
-----Original Message----- From: centos-bounces@centos.org [mailto:centos-bounces@centos.org] On Behalf Of Davide Cittaro Sent: Tuesday, November 25, 2008 6:11 AM To: CentOS mailing list Subject: Re: [CentOS] bioinformatics repository?
Hello John, and thanks for the tips
On Nov 25, 2008, at 11:59 AM, John wrote:
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.
Unfortunately that repos is suitable for physics and not really for biology... :-( I found some useful rpm in FC6 repository but still I miss a lot of packages. What is strange is that lot of those packages are standard on less spread OS (I use Gentoo and FreeBSD)...
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.
That's interesting... is it a yum wrapper for apt-get or do I have to download .deb packages and resolve dependencies on my own?
Use a tool named Alien to convert the debian packages to RPM format. Although be warned I have not had all that much success with doing it. It will either work or not work on installation of the rpm. Alien not only Converts .deb to .rpm, but can also do converts for other operating systems package formats as long as you have the correct libs installed.
http://www.linuxdocs.org/HOWTOs/RPM-for-Unix-HOWTO-8.html
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.
On Nov 25, 2008, at 12:08 PM, Vandaman wrote:
These look like BioRpms to me BioRPMS :- Bioinformatics RPMs Repository http://informatics.umdnj.edu/BioRPMs/
Ouch! I've missed this!
thanks
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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
-
Davide Cittaro -
John -
Kai Schaetzl -
Marcelo M. Garcia -
Sorin Srbu -
Tony Schreiner -
Vandaman