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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
author iuc
date Sun, 14 Jan 2024 11:00:33 +0000
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10 The reference for Trimmomatic is: 10 The reference for Trimmomatic is:
11 11
12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer 12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
13 for Illumina Sequence Data. Bioinformatics, btu170. 13 for Illumina Sequence Data. Bioinformatics, btu170.
14 14
15 Automated installation
16 ======================
17
18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
19 and the trimmomatic program and data, and setting the appropriate environment
20 variables.
21
22 Controlling the available memory 15 Controlling the available memory
23 ================================ 16 ================================
24 17
25 The default amount of memory avilable to trimmomatic is set to 8GB. 18 The default amount of memory avilable to trimmomatic is set to 8GB.
26 To change the default amount of memory you can set the environment variable 19 To change the default amount of memory you can set the environment variable
30 23
31 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>`` 24 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
32 25
33 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``. 26 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
34 27
35 Manual Installation
36 ===================
37
38 There are two files to install:
39
40 - ``trimmomatic.xml`` (the Galaxy tool definition)
41 - ``trimmomatic.sh`` (the shell script wrapper)
42
43 The suggested location is in a ``tools/trimmomatic/`` folder. You will then
44 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
45 by adding the line:
46
47 <tool file="trimmomatic/trimmomatic.xml" />
48
49 You will also need to install trimmomatic 0.38:
50
51 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
52
53 The tool wrapper uses the following environment variables in order to find the
54 appropriate files:
55
56 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
57 ``trimmomatic-0.36.jar`` file
58 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
59 sequence files (used by the ``ILLUMINACLIP`` option).
60
61 If you want to run the functional tests, copy the sample test files under
62 sample test files under Galaxy's ``test-data/`` directory. Then:
63
64 ./run_tests.sh -id trimmomatic
65
66 You will need to have set the environment variables above.
67
68 History 28 History
69 ======= 29 =======
70 30
71 ========== ====================================================================== 31 ============== ================================================================
72 Version Changes 32 Version Changes
73 ---------- ---------------------------------------------------------------------- 33 -------------- ----------------------------------------------------------------
74 0.39 - Update to Trimmomatic 0.39. 34 0.39+galaxy1 - Relocated to the ``tools-iuc`` repository
75 0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is 35 0.39 - Update to Trimmomatic 0.39.
76 supported across both Linux and MacOS platforms. 36 0.38.1 - Bug fix: add dependency on ``coreutils`` so that
77 0.38.0 - Update to Trimmomatic 0.38. 37 ``readlink -e`` is supported across both Linux and MacOS
78 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` 38 platforms.
79 and ``fastqsolexa`` input types 39 0.38.0 - Update to Trimmomatic 0.38.
80 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool 40 0.36.6 - Added trimlog and log outputs; add support for
81 dependencies 41 ``fastqillumina`` and ``fastqsolexa`` input types
82 0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP 42 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve
83 - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP 43 tool dependencies
84 in palindrome mode 44 0.36.4 - Add option to provide custom adapter sequences for
85 0.36.3 - Fix naming of output collections. Instead of all outputs being called 45 ILLUMINACLIP
86 "Trimmomatic on collection NN" these will now be called "Trimmomatic 46 - Add options ``minAdapterLength`` and ``keepBothReads`` for
87 on collection NN: paired" or "Trimmomatic on collection NN: unpaired". 47 ILLUMINACLIP in palindrome mode
88 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input 48 0.36.3 - Fix naming of output collections. Instead of all outputs being
89 the output will also be fastqsanger.gz. 49 called "Trimmomatic on collection NN" these will now be called
90 - Use $_JAVA_OPTIONS to customize memory requirements. 50 "Trimmomatic on collection NN: paired" or "Trimmomatic on
91 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version 51 collection NN: unpaired".
92 is still supported for now). 52 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as
93 0.36.0 - Update to Trimmomatic 0.36. 53 input the output will also be fastqsanger.gz.
94 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. 54 - Use $_JAVA_OPTIONS to customize memory requirements.
95 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input 55 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed
96 can be dataset collection, in which case tool also outputs dataset 56 version is still supported for now).
97 collections) and improve order and naming of output files. 57 0.36.0 - Update to Trimmomatic 0.36.
98 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use 58 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
99 at runtime (default is 6). 59 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections
100 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files 60 (input can be dataset collection, in which case tool also
101 into the XML wrapper. 61 outputs dataset collections) and improve order and naming of
102 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and 62 output files.
103 set the environment. 63 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads
104 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) 64 to use at runtime (default is 6).
105 with tool iteration appended (i.e. ``.1``). 65 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code
106 0.0.4 - Specify '-threads 6' in <command> section. 66 adapter files into the XML wrapper.
107 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. 67 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32
108 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires 68 automatically and set the environment.
109 the trimmomatic_adapters.loc file; sample version is supplied) plus 69 - Update tool versioning to use Trimmomatic version number (i.e.
110 cosmetic updates to wording and help text for some options. 70 ``0.32``) with tool iteration appended (i.e. ``.1``).
111 0.0.1 - Initial version 71 0.0.4 - Specify '-threads 6' in <command> section.
112 ========== ====================================================================== 72 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of
73 trimmomatic.
74 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences
75 (requires the trimmomatic_adapters.loc file; sample version is
76 supplied) plus cosmetic updates to wording and help text for
77 some options.
78 0.0.1 - Initial version
79 ============== ================================================================
113 80
114 81
115 Credits 82 Credits
116 ======= 83 =======
117 84
118 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). 85 This wrapper was originally developed and maintained by Peter Briggs
86 (@pjbriggs).
119 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 87 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed
120 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and 88 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
121 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. 89 Jelle Scholtalbers (@scholtalbers) contributed additional options to
90 ILLUMINACLIP.
122 Matthias Bernt (@bernt-matthias) added log and trimlog output. 91 Matthias Bernt (@bernt-matthias) added log and trimlog output.
123 Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform 92 Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
124 support across Linux and MacOS. 93 support across Linux and MacOS.
125 Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39. 94 Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.
95 Peter Briggs wishes to acknowledge the help from Matthia Bernt
96 (@bernt-matthias) with relocating the tool in the IUC tool repository,
97 and the IUC for taking on responsibility for the tool.
126 98
127 Developers 99 Developers
128 ========== 100 ==========
129 101
130 This tool is developed on the following GitHub repository: 102 The Trimmomatic tool is now maintained as part of the ``tools-iuc`` repository
131 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic 103 on GitHub:
132 104 https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic
133 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
134 the ``package_trimmomatic.sh`` script.
135
136 105
137 Licence (MIT) 106 Licence (MIT)
138 ============= 107 =============
139 108
140 Permission is hereby granted, free of charge, to any person obtaining a copy 109 Permission is hereby granted, free of charge, to any person obtaining a copy