# HG changeset patch
# User Oleg Shpynov <oleg.shpynov@gmail.com>
# Date 1445944842 -10800
# Node ID 5f97f28e65cac8fb51b026101830bb046ca50790

Initial commit

diff -r 000000000000 -r 5f97f28e65ca README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Oct 27 14:20:42 2015 +0300
@@ -0,0 +1,41 @@
+Galaxy Applications
+=================
+
+Quick setup
+------------
+
+* Download local copy of [galaxy](https://wiki.galaxyproject.org/Admin/GetGalaxy)
+* Checkout latest release: `git checkout release_15.01`
+* Create `config/galaxy.ini` as a copy of `config/galaxy.ini.sample`
+* Configure `tools_config_file`, `check_migrate_tools` properties
+* Minimal `tool_conf.xml`
+```
+    <?xml version='1.0' encoding='utf-8'?>
+    <toolbox>
+    <section id="getext" name="Get Data">
+        <tool file="data_source/upload.xml" />
+        <tool file="data_source/ucsc_tablebrowser.xml" />
+        <tool file="data_source/ebi_sra.xml" />
+        <tool file="data_source/biomart.xml" />
+    </section>
+    <section id="jetbrains" name="JetBrains tools">
+        <tool file="<PATH_TO_TOOLS>tools.xml" />
+    </section>
+    </toolbox>
+```
+
+Useful links
+------------
+* Galaxy
+ * [Develop apps](https://wiki.galaxyproject.org/Develop)
+ * [Add tool tutorial](https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial)
+ * [Tool config format](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax)
+ * [Quick reStructured text](http://docutils.sourceforge.net/docs/user/rst/quickref.html)
+ * [Main tools Shed resource](https://toolshed.g2.bx.psu.edu/repository)
+ * [Bed tools Shed example](https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_bedtools_2_24/tool_dependencies.xml)
+ * [Biostar Galaxy](https://biostar.usegalaxy.org)
+* Biolabs
+ * Our [homepage](http://beta-research.jetbrains.org/groups/biolabs)
+ * Our [wiki](http://biolabs.intellij.net)
+ * Our NIH powered [genome browser](http://genomebrowser.labs.intellij.net)
+ * [TeamCity](https://teamcity.jetbrains.com/project.html?projectId=Epigenome)
diff -r 000000000000 -r 5f97f28e65ca tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 27 14:20:42 2015 +0300
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<!--
+Tags information is here:
+https://wiki.galaxyproject.org/ToolDependenciesTagSets
+-->
+<tool_dependency>
+    <package name="epigenome" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_GenestackIntegration/lastSuccessful/genestack-Dev-all.jar</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/</destination_directory>
+                </action>
+                <!-- Set environment variable $EPIGENOME_JAR so Python script knows where to look -->
+                <action type="set_environment">
+                    <environment_variable name="EPIGENOME_JAR" action="set_to">$INSTALL_DIR/genestack-Dev-all.jar</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Downloads epigenome integration v0.0.1
+        </readme>
+    </package>
+</tool_dependency>
+
diff -r 000000000000 -r 5f97f28e65ca zinbra.py
--- /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)
+
diff -r 000000000000 -r 5f97f28e65ca zinbra.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zinbra.xml	Tue Oct 27 14:20:42 2015 +0300
@@ -0,0 +1,26 @@
+<tool id="zinbra" name="Zinbra" version="0.0.1">
+    <description>ChIP-Seq enrichment</description>
+    <requirements>
+        <requirement type="package" version="0.0.1">epigenome</requirement>
+    </requirements>
+    <stdio>
+        <!-- Wrapper ensures anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command interpreter="python">
+        zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
+    </command>
+    <inputs>
+        <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" />
+        <param name="genome" type="genomebuild" label="Genome build" description="Genome build used for alignment" />
+        <param name="bin" size="5" type="integer" value="200" label="Bin size" />
+        <param name="fdr" size="5" type="float" value="0.0001" label="FDR" />
+    </inputs>
+    <outputs>
+        <data name="result" format="bed" label="result.bed" />
+    </outputs>
+    <help>
+Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.
+    </help>
+</tool>