# HG changeset patch
# User pjbriggs
# Date 1585212767 14400
# Node ID d94aff5ee62311268e0b74dc90385108078fed10
# Parent  898b67846b47675128a192fc01049d3dce75c6fc
Version 0.38.1: add coreutils as dependency to fix tool issues with 'readlink -e' across platforms.

diff -r 898b67846b47 -r d94aff5ee623 README.rst
--- a/README.rst	Mon Jul 08 07:09:10 2019 -0400
+++ b/README.rst	Thu Mar 26 04:52:47 2020 -0400
@@ -46,9 +46,9 @@
 
     <tool file="trimmomatic/trimmomatic.xml" />
 
-You will also need to install trimmomatic 0.36:
+You will also need to install trimmomatic 0.38:
 
-- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
+- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
 
 The tool wrapper uses the following environment variables in order to find the
 appropriate files:
@@ -71,6 +71,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+0.38.1     - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is
+             supported across both Linux and MacOS platforms.
 0.38.0     - Update to Trimmomatic 0.38.
 0.36.6     - Added trimlog and log outputs; add support for ``fastqillumina``
              and ``fastqsolexa`` input types
@@ -117,6 +119,8 @@
 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP.
 Matthias Bernt (@bernt-matthias) added log and trimlog output.
+Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
+support across Linux and MacOS.
 
 Developers
 ==========
diff -r 898b67846b47 -r d94aff5ee623 trimmomatic.xml
--- a/trimmomatic.xml	Mon Jul 08 07:09:10 2019 -0400
+++ b/trimmomatic.xml	Thu Mar 26 04:52:47 2020 -0400
@@ -1,10 +1,16 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.38.0">
+<tool id="trimmomatic" name="Trimmomatic" version="0.38.1">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>
   </macros>
   <requirements>
     <requirement type="package" version="0.38">trimmomatic</requirement>
+    <!--
+	Coreutils required for 'readlink -e' work across platforms
+	See similar fix for snpSift
+	https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
+    -->
+    <requirement type="package" version="8.25">coreutils</requirement>
   </requirements>
   <command detect_errors="aggressive"><![CDATA[
   @CONDA_TRIMMOMATIC_JAR_PATH@ &&
diff -r 898b67846b47 -r d94aff5ee623 trimmomatic_macros.xml
--- a/trimmomatic_macros.xml	Mon Jul 08 07:09:10 2019 -0400
+++ b/trimmomatic_macros.xml	Thu Mar 26 04:52:47 2020 -0400
@@ -3,6 +3,6 @@
        Set the path for the trimmomatic JAR and data files
        Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13
   -->
-  <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi</token>
-  <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -f \$(which trimmomatic)))/adapters; fi</token>
+  <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token>
+  <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token>
 </macros>