# 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 @@
+<!--
+Package for downloading latest successful development tools.
+Tags information is here:
+https://wiki.galaxyproject.org/ToolDependenciesTagSets
+-->
+<package name="integration_jar" version="0.0.1" prior_installation_required="True">
+    <install version="1.0">
+        <actions>
+            <action type="download_by_url">http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_Integration/lastSuccessful/integration-Dev-all.jar</action>
+            <action type="move_directory_files">
+                <source_directory>.</source_directory>
+                <destination_directory>$INSTALL_DIR/</destination_directory>
+            </action>
+            <!-- Set environment variable $INTEGRATION_JAR so Python script knows where to look -->
+            <action type="set_environment">
+                <environment_variable name="$INTEGRATION_JAR" action="set_to">$INSTALL_DIR/integration-Dev-all.jar</environment_variable>
+            </action>
+        </actions>
+    </install>
+    <readme>
+        Downloads epigenome integration JAR.
+    </readme>
+</package>
diff -r 7d532e820976 -r 617b5857ce96 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 28 20:08:20 2015 +0300
+++ b/tool_dependencies.xml	Thu Oct 29 11:57:02 2015 +0300
@@ -1,26 +1,6 @@
 <?xml version="1.0"?>
-<!--
-Tags information is here:
-https://wiki.galaxyproject.org/ToolDependenciesTagSets
--->
-<tool_dependency>
-    <package name="epigenome" version="0.0.1" prior_installation_required="True">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_Integration/lastSuccessful/integration-Dev-all.jar</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/</destination_directory>
-                </action>
-                <!-- Set environment variable $INTEGRATION_JAR so Python script knows where to look -->
-                <action type="set_environment">
-                    <environment_variable name="$INTEGRATION_JAR" action="set_to">$INSTALL_DIR/integration-Dev-all.jar</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Downloads epigenome integration JAR.
-        </readme>
-    </package>
+<tool_dependency xmlns:xi="http://www.w3.org/1999/XSL/Transform">
+    <xi:include href="../integration_jar.xml" parse="xml" xpointer=""/>
+    <!-- For galaxy repo layout -->
+    <xi:include href="integration_jar.xml" parse="xml" xpointer=""/>
 </tool_dependency>
-
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 @@
 <tool id="zinbra" name="Zinbra" version="0.0.1">
-    <description>ChIP-Seq enrichment</description>
+    <description>ChIP-Seq analysis</description>
     <requirements>
-        <requirement type="package" version="0.0.1">epigenome</requirement>
+        <requirement type="package" version="0.0.1">integration_jar</requirement>
     </requirements>
     <stdio>
         <!-- Wrapper ensures anything other than zero is an error -->
@@ -10,9 +10,9 @@
     </stdio>
     <command interpreter="python">
         #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
     </command>
     <inputs>
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)