# HG changeset patch
# User jetbrains
# Date 1539338706 14400
# Node ID eccf47de11928c9bb639b728b55badfdf72db2fa
# Parent  0bf15064d38ec8851956aab8cbdc790fa82c3af4
Deleted selected files

diff -r 0bf15064d38e -r eccf47de1192 README.md
--- a/README.md	Thu Nov 12 12:03:47 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-Release
-=======
-Release is just a snapshot of files from [development repo](https://github.com/JetBrains-Research/galaxy) application folder.
diff -r 0bf15064d38e -r eccf47de1192 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 12 12:03:47 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <!--
-    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>
-</tool_dependency>
diff -r 0bf15064d38e -r eccf47de1192 zinbra.xml
--- a/zinbra.xml	Thu Nov 12 12:03:47 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="zinbra" name="Zinbra" version="0.0.1">
-    <description>ChIP-Seq analysis</description>
-    <requirements>
-        <requirement type="package" version="0.0.1">integration_jar</requirement>
-    </requirements>
-    <stdio>
-        <!-- Wrapper ensures anything other than zero is an error -->
-        <exit_code range="1:"/>
-        <exit_code range=":-1"/>
-    </stdio>
-    <command interpreter="python">
-        #if $action.selection == "analyze"
-            zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
-        #else
-            zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
-        #end if
-    </command>
-    <inputs>
-        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
-        <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
-        <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
-        <conditional name="action">
-            <param name="selection" type="select" label="Action">
-                <option value="analyze">Compute enrichment of ChIP-Seq</option>
-                <option value="compare">Compare different ChIP-Seqs</option>
-            </param>
-            <when value="analyze">
-                <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/>
-            </when>
-            <when value="compare">
-                <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/>
-                <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/>
-            </when>
-        </conditional>
-    </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.
-https://github.com/JetBrains-Research/zinbra
-    </help>
-</tool>
diff -r 0bf15064d38e -r eccf47de1192 zinbra_wrapper.py
--- a/zinbra_wrapper.py	Thu Nov 12 12:03:47 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/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)