Mercurial > repos > pjbriggs > trimmomatic
annotate README.rst @ 3:f8a9a5eaca8a draft
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
| author | pjbriggs |
|---|---|
| date | Wed, 23 Sep 2015 08:59:23 -0400 |
| parents | a60283899c6d |
| children | 14d05f2d511d |
| rev | line source |
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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 | |
| 36 You will also need to install trimmomatic 0.32: | |
| 37 | |
| 38 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip | |
| 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 | |
| 44 ``trimmomatic-0.32.jar`` file | |
| 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 ---------- ---------------------------------------------------------------------- | |
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61 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input |
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62 can be dataset collection, in which case tool also outputs dataset |
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63 collections) and improve order and naming of output files. |
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64 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use |
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65 at runtime (default is 6). |
| 1 | 66 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files |
| 67 into the XML wrapper. | |
| 68 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and | |
| 69 set the environment. | |
| 70 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) | |
| 71 with tool iteration appended (i.e. ``.1``). | |
| 72 0.0.4 - Specify '-threads 6' in <command> section. | |
| 73 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. | |
| 74 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires | |
| 75 the trimmomatic_adapters.loc file; sample version is supplied) plus | |
| 76 cosmetic updates to wording and help text for some options. | |
| 77 0.0.1 - Initial version | |
| 78 ========== ====================================================================== | |
| 79 | |
| 80 | |
| 81 Developers | |
| 82 ========== | |
| 83 | |
| 84 This tool is developed on the following GitHub repository: | |
| 85 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic | |
| 86 | |
| 87 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 88 the ``package_trimmomatic.sh`` script. | |
| 89 | |
| 90 | |
| 91 Licence (MIT) | |
| 92 ============= | |
| 93 | |
| 94 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 95 of this software and associated documentation files (the "Software"), to deal | |
| 96 in the Software without restriction, including without limitation the rights | |
| 97 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 98 copies of the Software, and to permit persons to whom the Software is | |
| 99 furnished to do so, subject to the following conditions: | |
| 100 | |
| 101 The above copyright notice and this permission notice shall be included in | |
| 102 all copies or substantial portions of the Software. | |
| 103 | |
| 104 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 105 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 106 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 107 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 108 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 109 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 110 THE SOFTWARE. |