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comparison zinbra.py @ 1:8cbb06892b62

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Release version: https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5
author Oleg Shpynov <oleg.shpynov@gmail.com>
date Wed, 28 Oct 2015 11:28:49 +0300
parents 5f97f28e65ca
children 0eb50728861a
comparison
equal deleted inserted replaced
0:5f97f28e65ca 1:8cbb06892b62
11 argv = sys.argv[1:] 11 argv = sys.argv[1:]
12 print 'Arguments {0}'.format(argv) 12 print 'Arguments {0}'.format(argv)
13 genome, bed, bin, fdr = argv 13 genome, bed, bin, fdr = argv
14 14
15 # Configure main jar path 15 # Configure main jar path
16 epigenomeJar = os.environ.get("EPIGENOME_JAR") 16 jar = os.environ.get("EPIGENOME_JAR")
17 print 'Using JAR distributive file {0}'.format(epigenomeJar) 17 print 'Using JAR distributive file {0}'.format(jar)
18 18
19 print 'Genome file {0}'.format(genome) 19 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
20 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
21 subprocess.check_call(cmd, cwd=None, shell=True)
20 22
21 # See https://github.com/JetBrains-Research/zinbra for command line options 23 # See https://github.com/JetBrains-Research/zinbra for command line options
22 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions 24 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions
23 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ 25 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
24 'analyze -i {1} -bed result.bed -r {2} -b {3} -fdr {4}'.format(epigenomeJar, 26 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar,
25 bed, 27 bed,
26 genome, 28 bin, fdr)
27 bin, fdr)
28 print 'Launching zinbra: {0}'.format(cmd) 29 print 'Launching zinbra: {0}'.format(cmd)
29 subprocess.check_call(cmd, cwd=None, shell=True) 30 subprocess.check_call(cmd, cwd=None, shell=True)
30