--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmeth_wrapper.py	Thu Oct 29 12:04:47 2015 +0300
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import subprocess
+
+argv = sys.argv[1:]
+print 'Arguments {0}'.format(argv)
+
+# Check command
+if len(argv) == 4:
+    genome, fdr, action, bam = argv
+    assert action == "analyze"
+else:
+    genome, fdr, action, bam1, bam2 = argv
+    assert action == "compare"
+
+# Configure main jar path
+jar = os.environ.get("INTEGRATION_JAR")
+print 'Using JAR distributive file {0}'.format(jar)
+
+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/cmeth for command line options
+if action == "analyze":
+    cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \
+          'analyze -i {1} -r reference.2bit -fdr {2}'.format(jar, bam, fdr)
+else:
+    cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \
+          'compare -1 {1} -2 {2} -r reference.2bit -fdr {3}'.format(jar, bam1, bam2, fdr)
+print 'Launching cmeth: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)