Mercurial > repos > nilesh > rseqc

changeset 35:ff21a055413b

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Create lib directories during install, added README.txt
author lparsons
date Tue, 22 Jul 2014 16:52:10 -0400
parents 8fbd165f8835
children cd98580c35e3
files README.txt tool_dependencies.xml
diffstat 2 files changed, 27 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Tue Jul 22 16:52:10 2014 -0400
@@ -0,0 +1,24 @@
+== RSeQC Galaxy Wrapper ==
+
+This is a Galaxy wrapper for the RSeQC RNA-Seq QC package.
+
+** Installation **
+
+Installation from a tool shed provides the necessary tool dependencies, R, numpy, and RSeQC.
+
+Otherwise, make sure that R and the RSeQC scripts are in the path and run under the Galaxy environment.
+Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them.
+Restart the Galaxy server.
+
+Requires Python 2.7
+
+** Attribution **
+
+The RSeQC package and associated documentation can be found at: http://rseqc.sourceforge.net/
+
+The galaxy wrapper code was written by 
+    Nilesh Kavthekar, School of Engineering and Applied Sciences, University of Pennsylvania, Class of 2016
+Modified by 
+    Lance Parsons, Lewis-Sigler Institute for Integrative Genomics, Princeton University,
+    Björn Grüning, University of Freiburg, bjoern.gruening@gmail.com
+The development of the wrapper code is housed on BitBucket at: https://bitbucket.org/lance_parsons/rseqc_galaxy_wrapper
--- a/tool_dependencies.xml	Mon Nov 04 16:19:36 2013 -0500
+++ b/tool_dependencies.xml	Tue Jul 22 16:52:10 2014 -0400
@@ -4,11 +4,13 @@
         <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="rseqc" version="2.3.7">
         <install version="1.0">
             <actions>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
                 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">