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Version 0.38.1: add coreutils as dependency to fix tool issues with 'readlink -e' across platforms.
author pjbriggs
date Thu, 26 Mar 2020 04:52:47 -0400
parents 898b67846b47
children 32f1f56bd970
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13:898b67846b47 14:d94aff5ee623
44 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 44 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
45 by adding the line: 45 by adding the line:
46 46
47 <tool file="trimmomatic/trimmomatic.xml" /> 47 <tool file="trimmomatic/trimmomatic.xml" />
48 48
49 You will also need to install trimmomatic 0.36: 49 You will also need to install trimmomatic 0.38:
50 50
51 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip 51 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
52 52
53 The tool wrapper uses the following environment variables in order to find the 53 The tool wrapper uses the following environment variables in order to find the
54 appropriate files: 54 appropriate files:
55 55
56 - ``TRIMMOMATIC_DIR`` should point to the directory holding the 56 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
69 ======= 69 =======
70 70
71 ========== ====================================================================== 71 ========== ======================================================================
72 Version Changes 72 Version Changes
73 ---------- ---------------------------------------------------------------------- 73 ---------- ----------------------------------------------------------------------
74 0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is
75 supported across both Linux and MacOS platforms.
74 0.38.0 - Update to Trimmomatic 0.38. 76 0.38.0 - Update to Trimmomatic 0.38.
75 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` 77 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina``
76 and ``fastqsolexa`` input types 78 and ``fastqsolexa`` input types
77 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool 79 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool
78 dependencies 80 dependencies
115 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). 117 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs).
116 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 118 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed
117 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and 119 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
118 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. 120 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP.
119 Matthias Bernt (@bernt-matthias) added log and trimlog output. 121 Matthias Bernt (@bernt-matthias) added log and trimlog output.
122 Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
123 support across Linux and MacOS.
120 124
121 Developers 125 Developers
122 ========== 126 ==========
123 127
124 This tool is developed on the following GitHub repository: 128 This tool is developed on the following GitHub repository: