|
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
|
|
|
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.
|
