diff zinbra.py @ 1:8cbb06892b62

Release version: https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5

--- a/zinbra.py	Tue Oct 27 14:20:42 2015 +0300
+++ b/zinbra.py	Wed Oct 28 11:28:49 2015 +0300
@@ -13,18 +13,18 @@
 genome, bed, bin, fdr = argv
 
 # Configure main jar path
-epigenomeJar = os.environ.get("EPIGENOME_JAR")
-print 'Using JAR distributive file {0}'.format(epigenomeJar)
+jar = os.environ.get("EPIGENOME_JAR")
+print 'Using JAR distributive file {0}'.format(jar)
 
-print 'Genome file {0}'.format(genome)
+cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
+print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)
 
 # See https://github.com/JetBrains-Research/zinbra for command line options
 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions
 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
-      'analyze -i {1} -bed result.bed -r {2} -b {3} -fdr {4}'.format(epigenomeJar,
-                                                         bed,
-                                                         genome,
-                                                         bin, fdr)
+      'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar,
+                                                                                bed,
+                                                                                bin, fdr)
 print 'Launching zinbra: {0}'.format(cmd)
 subprocess.check_call(cmd, cwd=None, shell=True)
-