[Beowulf] New BioBrew Release

Glen Otero gotero at linuxprophet.com
Wed Feb 23 03:48:53 EST 2005


BioBrew-3.1 for x86 is here.

BioBrew is an open source Linux cluster distribution based on the 
popular Rocks (www.rocksclusters.org) cluster software and enhanced for 
bioinformatics. BioBrew includes popular cluster software e.g. MPICH, 
PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and 
Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, 
BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, 
MrBayes, and EMBOSS. A BioBrew DVD iso for x86 is freely available for 
download at BioBrew.org, a Bioinformatics.org sponsored and hosted 
website. README and INSTALL docs are also available on the website.

Features you'll find in this release that differ slightly from 
Rocks-3.1 include:
-Infiniband support from Mellanox (/usr/mellanox)
-Myrinet support with gm-2.0.11
-Virtual Machine Interface (VMI) 2.0. (/opt/vmi-2.0-gcc)
-mpich built for VMI (/opt/mpich-vmi-2.0-gcc)

Application upgrades for 3.1:
added modules back to distro with modulesenv 3.1.6-2
upgraded modulefiles to 1.0.2, including corrections to profile.d 
scripts submitted by Humberto Zuazaga
upgraded hmmer to 2.3.2-1
upgraded gromacs to 3.2.1-1
upgraded EMBOSS to 2.9.0-6; EMBOSS now installs to /usr/share and not 
/opt/BioBrew
upgraded NCBI BLAST with ncbitoools 6.1.0-2 and ncbi.tar.gz from 
10/20/04)
upgraded mpiBLAST to 1.3; mpiBLAST lives under /opt/NCBI/6.1.0/bin with 
the rest of the binaries
upgraded Phylip to 3.61-5 and separated it from EMBOSS

New applications:
MrBayes 3.0-1 has been added to BioBrew

BioBrew rolls are also here:
BioBrew rolls for Rocks-3.1 and Rocks-3.3 on x86 are also available on 
the website, as is a BioBrew roll for Rocks-3.3 on x86_64. The rolls 
contain the same bio apps as the full BioBrew release. But know that if 
you build a cluster with Rocks + BioBrew roll, you will not have access 
to the vmi, mpich-vmi, Infiniband, or Myrinet packages in the full 
BioBrew release. You will be relying on Rocks' Infiniband, mpich, and 
Myrinet support, which is slightly different than BioBrew's, when using 
these rolls. The BioBrew rolls include the SRPMS as well as the RPMS.

This is the first BioBrew release for x86_64:
The BioBrew roll for Rocks-3.3 on x86_64 includes the same apps as the 
x86 releases, except for Java and EMBOSS. EMBOSS is not included 
because Java for Rocks-3.3-x86_64 was not available at the time this 
release was built.

Future BioBrew development is likely to consist of BioBrew rolls only. 
I've got more apps planned. I'm also soliciting requests. Hint, hint...

Thanks to Joe Landman of Scalable Informatics and Luc Ducazu of 
BioLinux for the SRPMS they make available to the community, and from 
which I borrowed liberally. They helped make this release a reality. 
Thanks to the beta testers that downloaded the releases over the past 
few weeks and pointed out a few problems. Thanks to Aaron Darling and 
Humberto Zuazaga for their help with mpiBLAST and Modules, 
respectively. Special thanks to the folks running BioBrew mirrors!

Glen Otero Ph.D.
Linux Prophet
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