# HG changeset patch
# User oleg@oleg-desktop.times.labs.intellij.net
# Date 1446109022 -10800
# Node ID 617b5857ce96e8c1c245113d30c9a015dba055bc
# Parent 7d532e820976e0c90b1f4647ad280615d309c0a1
Snapshot 61f45be of dev repo
diff -r 7d532e820976 -r 617b5857ce96 integration_jar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integration_jar.xml Thu Oct 29 11:57:02 2015 +0300
@@ -0,0 +1,23 @@
+
+
+
+
+ http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_Integration/lastSuccessful/integration-Dev-all.jar
+
+ .
+ $INSTALL_DIR/
+
+
+
+ $INSTALL_DIR/integration-Dev-all.jar
+
+
+
+
+ Downloads epigenome integration JAR.
+
+
diff -r 7d532e820976 -r 617b5857ce96 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Oct 28 20:08:20 2015 +0300
+++ b/tool_dependencies.xml Thu Oct 29 11:57:02 2015 +0300
@@ -1,26 +1,6 @@
-
-
-
-
-
- http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_Integration/lastSuccessful/integration-Dev-all.jar
-
- .
- $INSTALL_DIR/
-
-
-
- $INSTALL_DIR/integration-Dev-all.jar
-
-
-
-
- Downloads epigenome integration JAR.
-
-
+
+
+
+
-
diff -r 7d532e820976 -r 617b5857ce96 zinbra.py
--- a/zinbra.py Wed Oct 28 20:08:20 2015 +0300
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#!/usr/bin/env python
-"""
-Python wrapper for zinbra.xml
-"""
-
-import os
-import sys
-import subprocess
-
-argv = sys.argv[1:]
-print 'Arguments {0}'.format(argv)
-
-# Check command
-if len(argv) == 5:
- genome, bin, fdr, action, bed = argv
- assert action == "analyze"
-else:
- genome, bin, fdr, action, bed1, bed2 = 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/zinbra for command line options
-if action == "analyze":
- cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
- 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr)
-else:
- cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
- 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr)
-print 'Launching zinbra: {0}'.format(cmd)
-subprocess.check_call(cmd, cwd=None, shell=True)
diff -r 7d532e820976 -r 617b5857ce96 zinbra.xml
--- a/zinbra.xml Wed Oct 28 20:08:20 2015 +0300
+++ b/zinbra.xml Thu Oct 29 11:57:02 2015 +0300
@@ -1,7 +1,7 @@
- ChIP-Seq enrichment
+ ChIP-Seq analysis
- epigenome
+ integration_jar
@@ -10,9 +10,9 @@
#if $action.selection == "analyze"
- zinbra.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
+ zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
#else
- zinbra.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
+ zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
#end if
diff -r 7d532e820976 -r 617b5857ce96 zinbra_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/zinbra_wrapper.py Thu Oct 29 11:57:02 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) == 5:
+ genome, bin, fdr, action, bed = argv
+ assert action == "analyze"
+else:
+ genome, bin, fdr, action, bed1, bed2 = 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/zinbra for command line options
+if action == "analyze":
+ cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
+ 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr)
+else:
+ cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
+ 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr)
+print 'Launching zinbra: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)