mpiblast
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- | ===== MPI Blast ===== | ||
- | Parallel implementation of NCBI's BLAST algorithm. | ||
- | http:// | ||
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- | * **--nfrags=10** Specifies how many database fragments you want to split the original database into. This should be equal to how many different nodes you want to run mpiblast on. | ||
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- | http:// | ||
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- | ===== Updating BLAST Databases ===== | ||
- | http:// | ||
- | ===== Notes on .ncbirc ==== | ||
- | Before running mpiBLAST, it is necessary to configure the shared and local storage paths that each node will use to access the database. A shared storage path is usually a path to a directory residing on a file server, such as NFS, AFS, or samba. The local storage path is typically a subdirectory within the /tmp directory, e.g. / | ||
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- | < | ||
- | Data=/ | ||
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- | [BLAST] | ||
- | BLASTDB=/ | ||
- | BLASTMAT=/ | ||
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- | [mpiBLAST] | ||
- | Shared=/ | ||
- | Local=/ | ||
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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, |