Commit e8a0e309 authored by Haarst, Jan van's avatar Haarst, Jan van
Browse files

Fixed number of threads

parent 7198ce2c
Pipeline #414 skipped
......@@ -29,7 +29,7 @@ if env.GetOption('num_jobs') <= 1:
env.SetOption('num_jobs', num_cpu)
num_threads = num_cpu/4
else:
num_threads = env.GetOption('num_jobs')
num_threads = num_cpu/env.GetOption('num_jobs')
print "running with -j", GetOption('num_jobs')
# Set number of simultaneous threads to something less than the number of CPUs
# /CPUs
......@@ -50,11 +50,11 @@ print "running with -j", GetOption('num_jobs')
#ASSEMBLY = "/home/assembly/dev_150/assemblies/clc-default/clc_contigs.fa"
#PREFIX = "clc"
ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
PREFIX = "allpaths_lg_454"
#ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
#PREFIX = "allpaths_lg_454"
#ASSEMBLY = "/home/assembly/dev_150/assemblies/S_lycopersicum_scaffolds.2.40.fa"
#PREFIX = "heinz"
ASSEMBLY = "/home/assembly/dev_150/assemblies/S_lycopersicum_scaffolds.2.40.fa"
PREFIX = "heinz"
#ASSEMBLY = "/home/assembly/progs/fermi/heinz/fmdef.p4.fa"
#PREFIX = "fermi"
......@@ -108,7 +108,7 @@ def addCommand(cmd, data):
#DATABASE
bwtFile = "%s.bwt" % PREFIX
bwtRes = addCommand("bwa index -a is -p %(TARGET)s %(SOURCE)s", {"TARGET": PREFIX, "SOURCE": ASSEMBLY})
bwtRes = addCommand("bwa index -a is -p %(BWT_PREFIX)s %(SOURCE)s", {"BWT_PREFIX": PREFIX, "TARGET": bwtFile, "SOURCE": ASSEMBLY})
#SETUP
......
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