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howto:bioinformatics:gnu-parallel [2018/09/07 12:59]
dane [Advanced Fault tolerant Blast] 		howto:bioinformatics:gnu-parallel [2023/04/17 12:40] (current)
ischeepers
Line 13: Line 13:
 #!/bin/bash #!/bin/bash
 #PBS -e /mnt/lustre/users/USERNAME/test_scripts/gnu_parallel.stderr.out #PBS -e /mnt/lustre/users/USERNAME/test_scripts/gnu_parallel.stderr.out
-#PBS -o /mnt/lsutre/users/USERNAME/test_scripts/gnu_parallel.stdout.out+#PBS -o /mnt/lustre/users/USERNAME/test_scripts/gnu_parallel.stdout.out
 #PBS -V #PBS -V
 #PBS -P PROGRAMMESHORTNAME #PBS -P PROGRAMMESHORTNAME
Line 24: Line 24:
 #PBS -mb #PBS -mb
  
-module add chpc/gnu/parallel-20160422+ 
 +module add chpc/BIOMODULES 
 +module add gnu-parallel
  
 WORKING_DIR=/mnt/lustre/users/USERNAME/test_scripts WORKING_DIR=/mnt/lustre/users/USERNAME/test_scripts
Line 120: Line 122:
 cd ${PBS_O_WORKDIR} cd ${PBS_O_WORKDIR}
  
-module add chpc/gnu/parallel-20160422 
 module add chpc/BIOMODULES module add chpc/BIOMODULES
-module add ncbi-blast/2.3.0/gcc+module add blast 
 +module add gnu-parallel 
 + 
 + 
 +#The module sets the env variable below 
 +# and provides the path to the databases 
 +#BLASTDB="/mnt/lustre/bsp/DB/BLAST" 
 +# To blast against eg, simply use -db nt 
 +# To see all databases, "ls $BLASTDB/*.?al"
  
-BLASTDB="/lustre/bsp/blast/nt/nt" 
 BLASTCMD=$(which blastn) BLASTCMD=$(which blastn)
-BLASTARGS="-evalue 0.005 -num_alignments 20 -outfmt 5 -num_threads 24"+BLASTARGS="-evalue 0.005 -num_alignments 20 -outfmt 5 -num_threads 24 -db nt"
 INPUTDIRS="DATE/*" INPUTDIRS="DATE/*"
  
-ls ${INPUTDIRS}/*.fasta | parallel -M --sshdelay 0.2 -j 1 -u --sshloginfile ${PBS_NODEFILE} "cd ${PBS_O_WORKDIR}; ${BLASTCMD} -db ${BLASTDB} -query {} ${BLASTARGS} -out {}.xml && gzip --best {} {}.xml"+ls ${INPUTDIRS}/*.fasta | parallel -M --sshdelay 0.2 -j 1 -u --sshloginfile ${PBS_NODEFILE} "cd ${PBS_O_WORKDIR}; ${BLASTCMD} -query {} ${BLASTARGS} -out {}.xml && gzip --best {} {}.xml"
 </file> </file>
  
Line 152: Line 160:
 cd ${PBS_O_WORKDIR} cd ${PBS_O_WORKDIR}
  
-module add chpc/gnu/parallel-20160422+
 module add chpc/BIOMODULES module add chpc/BIOMODULES
-module add ncbi-blast/2.3.0/gcc+module add blast 
 +module add gnu-parallel
  
-BLASTDBDIR="/lustre/bsp/blast/nt" +BLASTDB="/mnt/lustre/bsp/NCBI/BLAST" 
-BLASTDB="nt"+DB="nt"
 BLASTCMD=$(which blastn) BLASTCMD=$(which blastn)
 BLASTARGS="-evalue 0.005 -num_alignments 20 -outfmt 5 -num_threads 24" BLASTARGS="-evalue 0.005 -num_alignments 20 -outfmt 5 -num_threads 24"
Line 167: Line 176:
 for node in ${NODES} for node in ${NODES}
 do do
-  ssh ${node} "mkdir -p /dev/shm/${USER}/BLAST && cp -r ${BLASTDBDIR}/${BLASTDB}* /dev/shm/${USER}/BLAST && echo 'successfully added DBs on ${node}' || exit 1" &+  ssh ${node} "mkdir -p /dev/shm/${USER}/BLAST && cp -r ${BLASTDB}/${DB}* /dev/shm/${USER}/BLAST && echo 'successfully added DBs on ${node}' || exit 1" &
 done done
  
Line 270: Line 279:
 #PBS -r n #PBS -r n
  
-module add chpc/gnu/parallel-20160422+module add chpc/BIOMODULES 
 +module add gnu-parallel
  
 JOBSPERNODE=16 JOBSPERNODE=16
/app/dokuwiki/data/attic/howto/bioinformatics/gnu-parallel.1536317950.txt.gz · Last modified: 2021/12/09 16:42 (external edit)

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