Mercurial > repos > lparsons > htseq_count

changeset 12:62a1de8c8aae

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Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
author lparsons
date Mon, 11 Mar 2013 12:44:45 -0400
parents f320093f1e8e
children 30bb8acb77a4
files htseq-count.xml tool_dependencies.xml
diffstat 2 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/htseq-count.xml	Mon Dec 10 13:36:54 2012 -0500
+++ b/htseq-count.xml	Mon Mar 11 12:44:45 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>
--- 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>