# HG changeset patch
# User lparsons
# Date 1363020162 14400
# Node ID 08a11d1eaec6cbb3ae6b57429b24630ee73393bf
# Parent  0a835934d792c0cf8932a6e971c285725b47b412
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist

diff -r 0a835934d792 -r 08a11d1eaec6 htseq-count.xml
--- a/htseq-count.xml	Tue Mar 05 12:26:28 2013 -0500
+++ b/htseq-count.xml	Mon Mar 11 12:42:42 2013 -0400
@@ -1,9 +1,9 @@
-<tool id="htseq_count" name="htseq-count" version="0.3">
+<tool id="htseq_count" name="htseq-count" version="0.3.1">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
         <requirement type="package" version="1.6.2">numpy</requirement>
-        <requirement type="package" version="0.5.3p9">htseq</requirement>
+        <requirement type="package" version="0.5.4p1">htseq</requirement>
         <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="1.56.0">picard</requirement> 
     </requirements>
@@ -178,10 +178,6 @@
 comparative ChIP-Seq, the features might be binding regions from a pre-determined 
 list.
 
-**Paired-end Data MUST be sorted by QUERY NAME first**
-
-This tool requires that paired-end data be sorted by query name, which is NOT the default for Galaxy. Using the Picard Paired Read Mate Fixer with Query name sort FIRST is required for paired end data.
-
 
 Overlap Modes
 -------------
@@ -195,11 +191,13 @@
 .. image:: /static/images/count_modes.png
     :width: 500
 
+
 Strandedness
 ------------
 
 **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
 
+
 Output
 ------
 
diff -r 0a835934d792 -r 08a11d1eaec6 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 12:26:28 2013 -0500
+++ b/tool_dependencies.xml	Mon Mar 11 12:42:42 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>