# HG changeset patch
# User pjbriggs
# Date 1490099504 14400
# Node ID a923b799c77cf923d53c97d0a4bc5b9afda3bd87
# Parent  77dd0fe954c5e3e9194e22eabc89007b2046ef8e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).

diff -r 77dd0fe954c5 -r a923b799c77c README.rst
--- a/README.rst	Fri Feb 24 04:57:13 2017 -0500
+++ b/README.rst	Tue Mar 21 08:31:44 2017 -0400
@@ -19,6 +19,19 @@
 and the trimmomatic program and data, and setting the appropriate environment
 variables.
 
+Controlling the available memory
+================================
+
+The default amount of memory avilable to trimmomatic is set to 8GB.
+To change the default amount of memory you can set the environment variable
+``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
+set this is in the job_conf.xml file. To change the available memory to 6GB, a
+line like the below should be added:
+
+``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
+
+This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
+
 Manual Installation
 ===================
 
@@ -58,6 +71,9 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+0.36.3     - Fix naming of output collections. Instead of all outputs being called
+             "Trimmomatic on collection NN" these will now be called "Trimmomatic
+             on collection NN: paired" or "Trimmomatic on collection NN: unpaired".
 0.36.2     - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input
              the output will also be fastqsanger.gz.
            - Use $_JAVA_OPTIONS to customize memory requirements.
diff -r 77dd0fe954c5 -r a923b799c77c trimmomatic.xml
--- a/trimmomatic.xml	Fri Feb 24 04:57:13 2017 -0500
+++ b/trimmomatic.xml	Tue Mar 21 08:31:44 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.36.2">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.3">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>
@@ -175,12 +175,12 @@
     <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
       <filter>readtype['single_or_paired'] == 'se'</filter>
     </data>
-    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired">
+    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
       <filter>readtype['single_or_paired'] == "collection"</filter>
       <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
       <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
     </collection>
-      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired">
+      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
         <filter>readtype['single_or_paired'] == "collection"</filter>
         <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
         <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>