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comparison zinbra.py @ 2:0eb50728861a

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Released version: Updated intergration artifact downloading c585add5cb6f16dce315be256f72119fe530e8f5
author oleg@oleg-desktop.times.labs.intellij.net
date Wed, 28 Oct 2015 18:48:43 +0300
parents 8cbb06892b62
children 7d532e820976
comparison
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1:8cbb06892b62 2:0eb50728861a
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 jar = os.environ.get("EPIGENOME_JAR") 16 jar = os.environ.get("INTEGRATION_JAR")
17 print 'Using JAR distributive file {0}'.format(jar) 17 print 'Using JAR distributive file {0}'.format(jar)
18 18
19 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, 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) 20 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
21 subprocess.check_call(cmd, cwd=None, shell=True) 21 subprocess.check_call(cmd, cwd=None, shell=True)