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Old 11-25-2008, 08:12 AM
Davide Cittaro
 
Default 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?
Thanks
d
/*Davide CittaroCogentech - Consortium for Genomic Technologiesvia adamello, 1620139 MilanoItaly
tel.: +39(02)574303007e-mail:*davide.cittaro@ifom-ieo-campus.it*/
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Old 11-25-2008, 08:46 AM
"Sorin Srbu"
 
Default bioinformatics repository?

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
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Old 11-25-2008, 09:23 AM
Davide Cittaro
 
Default bioinformatics repository?

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
*/



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Old 11-25-2008, 09:59 AM
"John"
 
Default bioinformatics repository?

> -----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

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Old 11-25-2008, 10:08 AM
Vandaman
 
Default bioinformatics repository?

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.




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Old 11-25-2008, 10:11 AM
Davide Cittaro
 
Default 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?


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
*/



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Old 11-25-2008, 10:29 AM
Davide Cittaro
 
Default bioinformatics repository?

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
*/



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Old 11-25-2008, 10:31 AM
Kai Schaetzl
 
Default bioinformatics repository?

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

--
Kai Schätzl, Berlin, Germany
Get your web at Conactive Internet Services: http://www.conactive.com



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Old 11-25-2008, 10:56 AM
"Marcelo M. Garcia"
 
Default bioinformatics repository?

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

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Old 11-25-2008, 12:35 PM
"John"
 
Default bioinformatics repository?

> -----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

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