Commit b4bbf71a authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

Added outside environment, and fixed typo in FRC command.

parent 376aa7cb
......@@ -10,7 +10,7 @@ ONLY_PROCESS_IF_DONT_EXISTS = False
##########################
## CHECKING
##########################
env = Environment()
env = Environment(ENV = os.environ) # Add os.environ, otherwise PATH doesn't get picked up
env.SourceCode(".", None)
#env.Decider('timestamp-newer')
......@@ -32,14 +32,14 @@ env.Decider(my_decider)
############
ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
PREFIX = "allpaths_lg"
#ASSEMBLY = "/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta"
#PREFIX = "allpaths_lg"
#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"
......@@ -138,7 +138,7 @@ for fileType in data:
outName = "rc_%s" % bn
#Convert the mate pair data into paired-end format.
res = addCommand("revseq -sequence %(SOURCE)s -outseq %(OUTFILE)s -notag", {"TARGET": outName+'.fastq', "SOURCE": fileName, 'OUTFILE': outName})
res = addCommand("revseq -sequence %(SOURCE)s -outseq %(TARGET)s -notag", {"TARGET": outName+'.fastq', "SOURCE": fileName, 'OUTFILE': outName})
mapName = "%s.rc_%s.sai" % ( PREFIX, bn )
print " ", fileType , "REVSEQ", fileName, ">", [str(x) for x in res]
......@@ -235,7 +235,7 @@ for fileType in data:
# --genome-size $ESTIMATED_GENOME_SIZE \
# --output $OUTPUT_HEADER
outFRC = OUTPUT_HEADER + '_FRC.txt'
FCRcmd = "FCR \
FCRcmd = "FRC \
--pe-sam %(pesam)s \
--pe-min-insert %(peminins)d \
--pe-max-insert %(pemaxins)d \
......
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