diff tool_dependencies.xml @ 12:62a1de8c8aae

Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist

--- a/tool_dependencies.xml	Mon Dec 10 13:36:54 2012 -0500
+++ b/tool_dependencies.xml	Mon Mar 11 12:44:45 2013 -0400
@@ -16,14 +16,15 @@
         </readme>
     </package>
 
-    <package name="htseq" version="0.5.3p9">
+    <package name="htseq" version="0.5.4p1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
@@ -32,6 +33,7 @@
             Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
         </readme>
     </package>
+
     <package name="samtools" version="0.1.18">
         <install version="1.0">
             <actions>
@@ -55,6 +57,7 @@
             Compiling SAMtools requires the ncurses and zlib development libraries.
         </readme>
     </package>
+
     <package name="picard" version="1.56.0">
         <install version="1.0">
             <actions>