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author pjbriggs
date Tue, 09 Dec 2014 09:41:33 -0500
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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
18 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
19 the trimmomatic program and data, and setting the appropriate environment variables.
20
21 Manual Installation
22 ===================
23
24 There are two files to install:
25
26 - ``trimmomatic.xml`` (the Galaxy tool definition)
27 - ``trimmomatic.sh`` (the shell script wrapper)
28
29 The suggested location is in a ``tools/trimmomatic/`` folder. You will then
30 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
31 by adding the line:
32
33 <tool file="trimmomatic/trimmomatic.xml" />
34
35 You will also need to install trimmomatic 0.32:
36
37 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
38
39 The tool wrapper uses the following environment variables in order to find the
40 appropriate files:
41
42 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
43 ``trimmomatic-0.32.jar`` file
44 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
45 sequence files (used by the ``ILLUMINACLIP`` option).
46
47 If you want to run the functional tests, copy the sample test files under
48 sample test files under Galaxy's ``test-data/`` directory. Then:
49
50 ./run_tests.sh -id trimmomatic
51
52 You will need to have set the environment variables above.
53
54 History
55 =======
56
57 ========== ======================================================================
58 Version Changes
59 ---------- ----------------------------------------------------------------------
60 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files
61 into the XML wrapper.
62 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
63 set the environment.
64 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``)
65 with tool iteration appended (i.e. ``.1``).
66 0.0.4 - Specify '-threads 6' in <command> section.
67 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
68 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires
69 the trimmomatic_adapters.loc file; sample version is supplied) plus
70 cosmetic updates to wording and help text for some options.
71 0.0.1 - Initial version
72 ========== ======================================================================
73
74
75 Developers
76 ==========
77
78 This tool is developed on the following GitHub repository:
79 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
80
81 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
82 the ``package_trimmomatic.sh`` script.
83
84
85 Licence (MIT)
86 =============
87
88 Permission is hereby granted, free of charge, to any person obtaining a copy
89 of this software and associated documentation files (the "Software"), to deal
90 in the Software without restriction, including without limitation the rights
91 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
92 copies of the Software, and to permit persons to whom the Software is
93 furnished to do so, subject to the following conditions:
94
95 The above copyright notice and this permission notice shall be included in
96 all copies or substantial portions of the Software.
97
98 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
99 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
100 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
101 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
102 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
103 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
104 THE SOFTWARE.