diff tool_dependencies.xml @ 0:6231ae8f87b8

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Feb 11 08:29:02 2015 -0500
@@ -0,0 +1,75 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="zlib" version="1.2.8">
+    <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="python3" version="3.4.1">
+    <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+    
+  <package name="mimodd" version="0.1.5.2">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.2.tar.gz</action>
+        <action type="set_environment_for_install">
+          <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="python3" version="3.4.1" />
+          </repository>
+        </action>
+        <action type="set_environment_for_install">
+          <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="zlib" version="1.2.8" />
+          </repository>
+        </action>
+        <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
+      <!-- remove the plain python symlink from the venv to avoid its 
+           accidental use by Galaxy, MiModD uses python3 explicitly -->
+        <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
+      <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
+        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
+      <!-- make MiModD's wrapped binaries executable -->
+        <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
+        
+        
+        <action type="set_environment">
+      <!-- make the mimodd entry script discoverable -->
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
+      <!-- clear $PYTHONPATH and $PYTHONHOME -->
+          <environment_variable action="set_to" name="PYTHONPATH" />
+          <environment_variable action="set_to" name="PYTHONHOME" />
+      <!-- propagate $LD_LIBRARY_PATH -->    
+          <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
+        </action>
+        
+        
+      </actions>
+    </install>
+    <readme>
+Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
+Home-page: http://sourceforge.net/projects/mimodd/
+Author: Wolfgang Maier
+Author-email: [e-mail]
+License: GPL
+Download-URL: http://sourceforge.net/projects/mimodd/
+
+MiModD - Identify Mutations from Whole-Genome Sequencing Data
+*************************************************************
+        
+MiModD is an integrated solution for efficient and user-friendly analysis of 
+whole-genome sequencing (WGS) data from laboratory model organisms. 
+It enables geneticists to identify the genetic mutations present in an organism 
+starting from just raw WGS read data and a reference genome without the help of 
+a trained bioinformatician.
+
+MiModD is designed for good performance on standard hardware and enables WGS 
+data analysis for most model organisms on regular desktop PCs.
+
+MiModD can be installed under Linux and Mac OS with minimal software 
+requirements and a simple setup procedure. As a standalone package it can be 
+used from the command line, but can also be integrated seamlessly and easily 
+into any local installation of a Galaxy bioinformatics server providing a 
+graphical user interface, database management of results and simple composition 
+of analysis steps into workflows.
+    </readme>
+  </package>
+</tool_dependency>