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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 213668d2e5a61c806ad992c201ae6e304c6e0965-dirty
author sanbi-uwc
date Mon, 23 Jan 2017 06:31:29 -0500
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children 642a39a927c9
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1 Trimmomatic: flexible read trimming tool for Illumina NGS data
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2 ==============================================================
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4 Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
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5 manipluating Illumina FASTQ files (both single and paired-end).
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7 Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
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8 http://www.usadellab.org/cms/index.php?page=trimmomatic
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10 The reference for Trimmomatic is:
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12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
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13 for Illumina Sequence Data. Bioinformatics, btu170.
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15 Automated installation
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16 ======================
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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.
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22 Manual Installation
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23 ===================
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25 There are two files to install:
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27 - ``trimmomatic.xml`` (the Galaxy tool definition)
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28 - ``trimmomatic.sh`` (the shell script wrapper)
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30 The suggested location is in a ``tools/trimmomatic/`` folder. You will then
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31 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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32 by adding the line:
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34 <tool file="trimmomatic/trimmomatic.xml" />
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36 You will also need to install trimmomatic 0.36:
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38 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
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40 The tool wrapper uses the following environment variables in order to find the
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41 appropriate files:
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43 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
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44 ``trimmomatic-0.36.jar`` file
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45 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
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46 sequence files (used by the ``ILLUMINACLIP`` option).
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48 If you want to run the functional tests, copy the sample test files under
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49 sample test files under Galaxy's ``test-data/`` directory. Then:
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51 ./run_tests.sh -id trimmomatic
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53 You will need to have set the environment variables above.
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54
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55 History
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56 =======
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57
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58 ========== ======================================================================
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59 Version Changes
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60 ---------- ----------------------------------------------------------------------
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61 0.36.0 - Update to Trimmomatic 0.36.
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62 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
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63 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input
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64 can be dataset collection, in which case tool also outputs dataset
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65 collections) and improve order and naming of output files.
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66 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
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67 at runtime (default is 6).
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68 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files
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69 into the XML wrapper.
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70 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
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71 set the environment.
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72 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``)
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73 with tool iteration appended (i.e. ``.1``).
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74 0.0.4 - Specify '-threads 6' in <command> section.
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75 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
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76 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires
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77 the trimmomatic_adapters.loc file; sample version is supplied) plus
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78 cosmetic updates to wording and help text for some options.
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79 0.0.1 - Initial version
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80 ========== ======================================================================
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81
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83 Developers
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84 ==========
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85
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86 This tool is developed on the following GitHub repository:
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87 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
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88
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89 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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90 the ``package_trimmomatic.sh`` script.
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91
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92
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93 Licence (MIT)
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94 =============
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95
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96 Permission is hereby granted, free of charge, to any person obtaining a copy
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97 of this software and associated documentation files (the "Software"), to deal
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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98 in the Software without restriction, including without limitation the rights
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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99 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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100 copies of the Software, and to permit persons to whom the Software is
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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101 furnished to do so, subject to the following conditions:
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102
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103 The above copyright notice and this permission notice shall be included in
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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104 all copies or substantial portions of the Software.
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105
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106 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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107 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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108 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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109 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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110 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
d8975856862e planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153
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111 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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112 THE SOFTWARE.