# HG changeset patch
# User pjbriggs
# Date 1585147413 0
# Node ID d300b1888cef2788bdaedc666fbec6349c595627
# Parent ed7f4b065bb05c3f263b38d211fe4fd6dc4a0bcd
Uploaded bugfix version 0.38.1 for testing
diff -r ed7f4b065bb0 -r d300b1888cef README.rst
--- a/README.rst Mon Jul 08 06:35:08 2019 -0400
+++ b/README.rst Wed Mar 25 14:43:33 2020 +0000
@@ -46,9 +46,9 @@
-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 ed7f4b065bb0 -r d300b1888cef trimmomatic.xml
--- a/trimmomatic.xml Mon Jul 08 06:35:08 2019 -0400
+++ b/trimmomatic.xml Wed Mar 25 14:43:33 2020 +0000
@@ -1,10 +1,15 @@
-
+
flexible read trimming tool for Illumina NGS data
trimmomatic_macros.xml
- trimmomatic
+ trimmomatic
+ coreutils
- if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -f \$(which trimmomatic))); fi
- if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -f \$(which trimmomatic)))/adapters; fi
+ if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi
+ if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi