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mpiblast [2010/01/29 09:34] – 172.26.0.166mpiblast [2010/01/29 09:38] – 172.26.0.166
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   * http://wiki.bioinformatics.ucdavis.edu/index.php/MPI_Blast   * http://wiki.bioinformatics.ucdavis.edu/index.php/MPI_Blast
-  * OpenMPI FAQ: http://www.open-mpi.org/faq/ 
  
 <code>$ mpiformatdb -i drosoph.nt -p F --nfrags=12</code> <code>$ mpiformatdb -i drosoph.nt -p F --nfrags=12</code>
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 The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, be sure to format all databases with mpiformatdb rather than formatdb. The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, be sure to format all databases with mpiformatdb rather than formatdb.
- 
-===== wwwblast ===== 
-http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/wwwblast/ 
  
  
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   * http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-August/000988.html   * http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-August/000988.html
   * https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2008-February/029231.html   * https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2008-February/029231.html
- 
 ==== Incorrect mpiBLAST Version ==== ==== Incorrect mpiBLAST Version ====
-You're not crazy, it's a known issue: http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-February/000933.html 
 <code>$ rpmquery -a mpiblast     <code>$ rpmquery -a mpiblast    
 mpiblast-1.5.0-pio mpiblast-1.5.0-pio
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 mpiblast version 1.4.0 mpiblast version 1.4.0
 </code> </code>
 +You're not crazy, it's a known issue. 1.5.0 reports as 1.4.0: http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-February/000933.html
  
 ===== Links ===== ===== Links =====
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   * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl   * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
   * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/roll-documentation/bio/5.2/mpiblast_usage.html   * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/roll-documentation/bio/5.2/mpiblast_usage.html
 +  * wwwblast: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/wwwblast/