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Version that supports Trimmomatic 0.36.
author pjbriggs
date Thu, 14 Jul 2016 09:17:38 -0400
parents f8a9a5eaca8a
children f80107cdc406
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3:f8a9a5eaca8a 4:14d05f2d511d
31 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 31 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
32 by adding the line: 32 by adding the line:
33 33
34 <tool file="trimmomatic/trimmomatic.xml" /> 34 <tool file="trimmomatic/trimmomatic.xml" />
35 35
36 You will also need to install trimmomatic 0.32: 36 You will also need to install trimmomatic 0.36:
37 37
38 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip 38 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
39 39
40 The tool wrapper uses the following environment variables in order to find the 40 The tool wrapper uses the following environment variables in order to find the
41 appropriate files: 41 appropriate files:
42 42
43 - ``TRIMMOMATIC_DIR`` should point to the directory holding the 43 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
44 ``trimmomatic-0.32.jar`` file 44 ``trimmomatic-0.36.jar`` file
45 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter 45 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
46 sequence files (used by the ``ILLUMINACLIP`` option). 46 sequence files (used by the ``ILLUMINACLIP`` option).
47 47
48 If you want to run the functional tests, copy the sample test files under 48 If you want to run the functional tests, copy the sample test files under
49 sample test files under Galaxy's ``test-data/`` directory. Then: 49 sample test files under Galaxy's ``test-data/`` directory. Then:
56 ======= 56 =======
57 57
58 ========== ====================================================================== 58 ========== ======================================================================
59 Version Changes 59 Version Changes
60 ---------- ---------------------------------------------------------------------- 60 ---------- ----------------------------------------------------------------------
61 0.36.0 - Update to Trimmomatic 0.36.
62 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
61 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input 63 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input
62 can be dataset collection, in which case tool also outputs dataset 64 can be dataset collection, in which case tool also outputs dataset
63 collections) and improve order and naming of output files. 65 collections) and improve order and naming of output files.
64 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use 66 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
65 at runtime (default is 6). 67 at runtime (default is 6).