BIRCH
HPC Blast -
Technical Description
update October 3, 2025

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SUMMARY

If your institution has a cluster of High Performance Compute nodes with local copies of BLAST databases, this section tells how to add a button to BLAST search menus in bldna and blprotein.
How it works

All BLAST local BioLegato .blmenu files have a correspondng .blinclude file, found in $BIRCH/local/dat. If the .blinclude file exists a button is added to the BioLegato menu. If the .blincude file does not exist, no button will be added. The PCD code in the .blinclude file tells BioLegato to run bl_run_hpc.sh to perform the blast search. bl_run_hpc.sh takes care of all steps needed to run the corresponding BLAST command on the remote HPC node.



Consequently, you should not have to change the .blmenu files or the .blinclude files. At each BIRCH site, the only thing you should have to change is bl_run_hpc.sh. This bash script will have to be modified for the specific setup of how to run programs on your HPC nodes.

Example

BLASTPlocal.blmenu has an @include statement that tells BioLegato to insert the contents of BLASTPlocalHPC.include at the corresponding place in the .blmenu file. The included PCD code tells BioLegato to run BLASTP on the remote server.

$BIRCH/dat/blprotein/PCD/Database/BLASTPlocal.blmenu
panel
    var "Run"
        type        button
        label       "Run"
        shell       "(blastp -query %in1% %DBASE% -task %SEARCHTASK% -matrix %MATRIX% -evalue %EVALUE%  -num_threads %THREADS% %WORD% %SEG% %LMASK% %SMASK% %EQUERY% %OQUERY% %COMP% -outfmt 11 -max_target_seqs %MAXDISP% -out %in1%.blastp.asn1; %WRITEREPORT% %WRITETSV% %WRITEXML% %EMAIL% rm %in1% %in1%.blastp.asn1)& "
        close       true

    # If this file exists and is not empty, a button will be added to run the search on a remote server
    @include   $BIRCH/local/dat/blprotein/PCD/Database/BLASTPlocalHPC.blinclude

    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/NCBI/blastp.help"
        close       false


$BIRCH/local/dat/PCD/Database/BLASTPlocalHPC.blinclude
var "RunRemote"
    type        button
    label       "Run on BLAST server"
    shell       "(bl_run_hpc.sh blastp -query %in1% %DBASE% -task %SEARCHTASK% -matrix %MATRIX% -evalue %EVALUE%  -num_threads %THREADS% %WORD% %SEG% %LMASK% %SMASK% %EQUERY% %OQUERY% %COMP% -outfmt 11 -max_target_seqs %MAXDISP% -out %in1%.blastp.asn1 -parse_deflines; %WRITEREPORT% %WRITETSV% %WRITEXML% %EMAIL% rm %in1% %in1%.blastp.asn1)& "
    close       true


Assumptions



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