diff htseq-count.xml @ 6:08a11d1eaec6

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

--- 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
 ------