Mercurial > repos > pjbriggs > trimmomatic
annotate README.rst @ 6:141bba0e9a77 draft
Uploaded v0.36.2 (adds support for compressed fastq inputs)
author | pjbriggs |
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date | Fri, 24 Feb 2017 05:12:32 -0500 |
parents | f80107cdc406 |
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1 | 1 Trimmomatic: flexible read trimming tool for Illumina NGS data |
2 ============================================================== | |
3 | |
4 Galaxy tool wrapper for the Trimmomatic program, which provides various functions for | |
5 manipluating Illumina FASTQ files (both single and paired-end). | |
6 | |
7 Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university | |
8 http://www.usadellab.org/cms/index.php?page=trimmomatic | |
9 | |
10 The reference for Trimmomatic is: | |
11 | |
12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer | |
13 for Illumina Sequence Data. Bioinformatics, btu170. | |
14 | |
15 Automated installation | |
16 ====================== | |
17 | |
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18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper |
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19 and the trimmomatic program and data, and setting the appropriate environment |
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20 variables. |
1 | 21 |
22 Manual Installation | |
23 =================== | |
24 | |
25 There are two files to install: | |
26 | |
27 - ``trimmomatic.xml`` (the Galaxy tool definition) | |
28 - ``trimmomatic.sh`` (the shell script wrapper) | |
29 | |
30 The suggested location is in a ``tools/trimmomatic/`` folder. You will then | |
31 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
32 by adding the line: | |
33 | |
34 <tool file="trimmomatic/trimmomatic.xml" /> | |
35 | |
4 | 36 You will also need to install trimmomatic 0.36: |
1 | 37 |
4 | 38 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip |
1 | 39 |
40 The tool wrapper uses the following environment variables in order to find the | |
41 appropriate files: | |
42 | |
43 - ``TRIMMOMATIC_DIR`` should point to the directory holding the | |
4 | 44 ``trimmomatic-0.36.jar`` file |
1 | 45 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter |
46 sequence files (used by the ``ILLUMINACLIP`` option). | |
47 | |
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: | |
50 | |
51 ./run_tests.sh -id trimmomatic | |
52 | |
53 You will need to have set the environment variables above. | |
54 | |
55 History | |
56 ======= | |
57 | |
58 ========== ====================================================================== | |
59 Version Changes | |
60 ---------- ---------------------------------------------------------------------- | |
6
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61 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input |
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62 the output will also be fastqsanger.gz. |
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63 - Use $_JAVA_OPTIONS to customize memory requirements. |
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Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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64 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version |
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65 is still supported for now). |
4 | 66 0.36.0 - Update to Trimmomatic 0.36. |
67 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. | |
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68 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input |
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69 can be dataset collection, in which case tool also outputs dataset |
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70 collections) and improve order and naming of output files. |
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71 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use |
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72 at runtime (default is 6). |
1 | 73 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files |
74 into the XML wrapper. | |
75 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and | |
76 set the environment. | |
77 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) | |
78 with tool iteration appended (i.e. ``.1``). | |
79 0.0.4 - Specify '-threads 6' in <command> section. | |
80 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. | |
81 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires | |
82 the trimmomatic_adapters.loc file; sample version is supplied) plus | |
83 cosmetic updates to wording and help text for some options. | |
84 0.0.1 - Initial version | |
85 ========== ====================================================================== | |
86 | |
87 | |
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88 Credits |
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89 ======= |
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90 |
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91 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). |
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92 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed |
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93 support for gz compressed FastQ files. |
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94 |
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95 |
1 | 96 Developers |
97 ========== | |
98 | |
99 This tool is developed on the following GitHub repository: | |
100 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic | |
101 | |
102 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
103 the ``package_trimmomatic.sh`` script. | |
104 | |
105 | |
106 Licence (MIT) | |
107 ============= | |
108 | |
109 Permission is hereby granted, free of charge, to any person obtaining a copy | |
110 of this software and associated documentation files (the "Software"), to deal | |
111 in the Software without restriction, including without limitation the rights | |
112 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
113 copies of the Software, and to permit persons to whom the Software is | |
114 furnished to do so, subject to the following conditions: | |
115 | |
116 The above copyright notice and this permission notice shall be included in | |
117 all copies or substantial portions of the Software. | |
118 | |
119 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
120 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
121 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
122 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
123 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
124 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
125 THE SOFTWARE. |