Bug 111807 - Update ncbi-tools to patch in optional mpi support if desired.
Bug#: 111807 Product:  Gentoo Linux Version: unspecified Platform: All
OS/Version: Linux Status: RESOLVED Severity: enhancement Priority: P2
Resolution: FIXED Assigned To: ribosome@gentoo.org Reported By: gentoo@gecka.us
Component: Ebuilds
URL: 
Summary: Update ncbi-tools to patch in optional mpi support if desired.
Keywords:  
Status Whiteboard: 
Opened: 2005-11-07 11:52 0000
Description:   Opened: 2005-11-07 11:52 0000 
I am an admin for a large University Cluster. We are testing the idea of moving
the cluster over to Gentoo as it has awsome development tools for biology
programs. As such I have built several ebuild files to compile as of yet
non-included programs (lamarc, r-project, etc)

I was very excited to see that somebody had already done the ncbi-tools package.
However, it appears that this package doesn't make use of the 'mpi' use flag to
compile in mpiBLAST. I have a working ebuild that is designed with out cluster
in mind (no non-x86 support) but it should be easy to see how I was able to get
mpiBLAST to patch and compile.

I will try and attach the ebuild I am using once I have submitted the report.

Reproducible: Always
Steps to Reproduce:

------- Comment #1 From Brady Catherman 2005-11-07 11:53:48 0000 ------- 
Created an attachment (id=72409) [details]
The hobbled together version of ncbi I am using now.

------- Comment #2 From Brady Catherman 2005-11-07 12:00:10 0000 ------- 
The web site for mpiBLAST is here:
http://mpiblast.lanl.gov/Downloads.Archive.html


Also, would there be interest in including my custom ebuild scripts in the main
repository? I have added oommf, r-project, s3 (Stochastic Spatial), lamarc,
pdsh, and I am sure that there will be dozens more where these came from.

------- Comment #3 From Olivier Fisette 2005-11-12 16:28:56 0000 ------- 
Hi Brady, 
 
I wanted to have a look at MPI blast during the week-end, but it seems the 
download site is down... I am definitely interested in including this in our 
NCBI tools distribution, however. If you can put the source archive for the 
package somewhere on the Web, I will mirror it on the Gentoo infrastructure.

------- Comment #4 From Brady Catherman 2005-11-12 20:18:16 0000 ------- 
(In reply to comment #3)
> Hi Brady, 
>  
> I wanted to have a look at MPI blast during the week-end, but it seems the 
> download site is down... I am definitely interested in including this in our 
> NCBI tools distribution, however. If you can put the source archive for the 
> package somewhere on the Web, I will mirror it on the Gentoo infrastructure. 

I have placed it on our local web server here. The URL is:
http://styx.ibest.uidaho.edu/mpiblast/mpiBLAST-1.4.0.tgz

The ebuild I am using should have a semi understandable walktrogh on
installation. There is also an included install file that should help.

Thanks for your help with this issue! Sorry I forgot to check and see if
mpiBLAST was available =)

------- Comment #5 From Olivier Fisette 2005-11-14 16:30:06 0000 ------- 
Thanks for your work, Brady. Your patch is now in Portage, and MPI BLAST seems 
to work great. 
 
alpha, sparc: 
 
I had to drop ~sparc and ~alpha from the ebuild. 
 
The alpha team needs to add MPI to its profiles' use.mask since there is no 
MPI library available on this arch. 
 
The sparc team needs to set the default virtual/mpi for sparc to 
sys-cluster/lam-mpi since the default sys-cluster/mpich isn't available on 
sparc. 
 
Thanks in advance,

------- Comment #6 From Fernando J. Pereda (RETIRED) 2005-11-15 07:39:03 0000 ------- 
mpi use.mask'd and re-keyworded ncbi-tools.

Cheers,
Ferdy

------- Comment #7 From Olivier Fisette 2005-11-16 08:54:03 0000 ------- 
Virtual was corrected on sparc, so I readded the keyword.