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Release version: https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5
author Oleg Shpynov <oleg.shpynov@gmail.com>
date Wed, 28 Oct 2015 11:28:49 +0300
parents 5f97f28e65ca
children 0eb50728861a
files README.md tool_dependencies.xml zinbra.py zinbra.xml
diffstat 4 files changed, 17 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Tue Oct 27 14:20:42 2015 +0300
+++ b/README.md	Wed Oct 28 11:28:49 2015 +0300
@@ -1,41 +1,7 @@
-Galaxy Applications
-=================
-
-Quick setup
-------------
+Release version
+===============
+https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5
 
-* 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)
+NOTE
+----
+Release is just a snapshot of files from development repo application folder.
--- a/tool_dependencies.xml	Tue Oct 27 14:20:42 2015 +0300
+++ b/tool_dependencies.xml	Wed Oct 28 11:28:49 2015 +0300
@@ -4,7 +4,7 @@
 https://wiki.galaxyproject.org/ToolDependenciesTagSets
 -->
 <tool_dependency>
-    <package name="epigenome" version="0.0.1">
+    <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_GenestackIntegration/lastSuccessful/genestack-Dev-all.jar</action>
--- a/zinbra.py	Tue Oct 27 14:20:42 2015 +0300
+++ b/zinbra.py	Wed Oct 28 11:28:49 2015 +0300
@@ -13,18 +13,18 @@
 genome, bed, bin, fdr = argv
 
 # Configure main jar path
-epigenomeJar = os.environ.get("EPIGENOME_JAR")
-print 'Using JAR distributive file {0}'.format(epigenomeJar)
+jar = os.environ.get("EPIGENOME_JAR")
+print 'Using JAR distributive file {0}'.format(jar)
 
-print 'Genome file {0}'.format(genome)
+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
 # 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)
+      'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar,
+                                                                                bed,
+                                                                                bin, fdr)
 print 'Launching zinbra: {0}'.format(cmd)
 subprocess.check_call(cmd, cwd=None, shell=True)
-
--- a/zinbra.xml	Tue Oct 27 14:20:42 2015 +0300
+++ b/zinbra.xml	Wed Oct 28 11:28:49 2015 +0300
@@ -13,7 +13,7 @@
     </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="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" />
     </inputs>
@@ -22,5 +22,6 @@
     </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>