--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zinbra.py	Tue Oct 27 14:20:42 2015 +0300
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+"""
+Python wrapper for zinbra.xml
+Usage: zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
+"""
+
+import os
+import sys
+import subprocess
+
+argv = sys.argv[1:]
+print 'Arguments {0}'.format(argv)
+genome, bed, bin, fdr = argv
+
+# Configure main jar path
+epigenomeJar = os.environ.get("EPIGENOME_JAR")
+print 'Using JAR distributive file {0}'.format(epigenomeJar)
+
+print 'Genome file {0}'.format(genome)
+
+# 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)
+print 'Launching zinbra: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)
+