Mercurial > repos > pjbriggs > trimmomatic
annotate README.rst @ 13:898b67846b47 draft
Updated to Trimmomatic 0.38.
| author | pjbriggs |
|---|---|
| date | Mon, 08 Jul 2019 07:09:10 -0400 |
| parents | 59054f086eca |
| children | d94aff5ee623 |
| rev | line source |
|---|---|
| 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 | |
|
2
a60283899c6d
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
1
diff
changeset
|
18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper |
|
a60283899c6d
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
1
diff
changeset
|
19 and the trimmomatic program and data, and setting the appropriate environment |
|
a60283899c6d
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
1
diff
changeset
|
20 variables. |
| 1 | 21 |
|
7
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
22 Controlling the available memory |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
23 ================================ |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
24 |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
25 The default amount of memory avilable to trimmomatic is set to 8GB. |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
26 To change the default amount of memory you can set the environment variable |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
27 ``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
28 set this is in the job_conf.xml file. To change the available memory to 6GB, a |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
29 line like the below should be added: |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
30 |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
31 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>`` |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
32 |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
33 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``. |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
34 |
| 1 | 35 Manual Installation |
| 36 =================== | |
| 37 | |
| 38 There are two files to install: | |
| 39 | |
| 40 - ``trimmomatic.xml`` (the Galaxy tool definition) | |
| 41 - ``trimmomatic.sh`` (the shell script wrapper) | |
| 42 | |
| 43 The suggested location is in a ``tools/trimmomatic/`` folder. You will then | |
| 44 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
| 45 by adding the line: | |
| 46 | |
| 47 <tool file="trimmomatic/trimmomatic.xml" /> | |
| 48 | |
| 4 | 49 You will also need to install trimmomatic 0.36: |
| 1 | 50 |
| 4 | 51 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip |
| 1 | 52 |
| 53 The tool wrapper uses the following environment variables in order to find the | |
| 54 appropriate files: | |
| 55 | |
| 56 - ``TRIMMOMATIC_DIR`` should point to the directory holding the | |
| 4 | 57 ``trimmomatic-0.36.jar`` file |
| 1 | 58 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter |
| 59 sequence files (used by the ``ILLUMINACLIP`` option). | |
| 60 | |
| 61 If you want to run the functional tests, copy the sample test files under | |
| 62 sample test files under Galaxy's ``test-data/`` directory. Then: | |
| 63 | |
| 64 ./run_tests.sh -id trimmomatic | |
| 65 | |
| 66 You will need to have set the environment variables above. | |
| 67 | |
| 68 History | |
| 69 ======= | |
| 70 | |
| 71 ========== ====================================================================== | |
| 72 Version Changes | |
| 73 ---------- ---------------------------------------------------------------------- | |
| 13 | 74 0.38.0 - Update to Trimmomatic 0.38. |
|
11
59054f086eca
Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents:
10
diff
changeset
|
75 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` |
|
59054f086eca
Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents:
10
diff
changeset
|
76 and ``fastqsolexa`` input types |
|
10
dfa082f84068
Uploaded version 0.36.5 (use conda to resolve tool dependencies)
pjbriggs
parents:
8
diff
changeset
|
77 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool |
|
dfa082f84068
Uploaded version 0.36.5 (use conda to resolve tool dependencies)
pjbriggs
parents:
8
diff
changeset
|
78 dependencies |
| 8 | 79 0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP |
| 80 - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP | |
| 81 in palindrome mode | |
|
7
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
82 0.36.3 - Fix naming of output collections. Instead of all outputs being called |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
83 "Trimmomatic on collection NN" these will now be called "Trimmomatic |
|
6eeacf19a38e
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents:
6
diff
changeset
|
84 on collection NN: paired" or "Trimmomatic on collection NN: unpaired". |
|
6
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
85 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input |
|
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
86 the output will also be fastqsanger.gz. |
|
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
87 - Use $_JAVA_OPTIONS to customize memory requirements. |
|
5
f80107cdc406
Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
4
diff
changeset
|
88 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version |
|
f80107cdc406
Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
4
diff
changeset
|
89 is still supported for now). |
| 4 | 90 0.36.0 - Update to Trimmomatic 0.36. |
| 91 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. | |
|
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
92 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input |
|
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
93 can be dataset collection, in which case tool also outputs dataset |
|
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
94 collections) and improve order and naming of output files. |
|
2
a60283899c6d
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
1
diff
changeset
|
95 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use |
|
a60283899c6d
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
1
diff
changeset
|
96 at runtime (default is 6). |
| 1 | 97 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files |
| 98 into the XML wrapper. | |
| 99 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and | |
| 100 set the environment. | |
| 101 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) | |
| 102 with tool iteration appended (i.e. ``.1``). | |
| 103 0.0.4 - Specify '-threads 6' in <command> section. | |
| 104 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. | |
| 105 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires | |
| 106 the trimmomatic_adapters.loc file; sample version is supplied) plus | |
| 107 cosmetic updates to wording and help text for some options. | |
| 108 0.0.1 - Initial version | |
| 109 ========== ====================================================================== | |
| 110 | |
| 111 | |
|
6
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
112 Credits |
|
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
113 ======= |
|
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
114 |
|
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
115 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). |
|
11
59054f086eca
Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents:
10
diff
changeset
|
116 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed |
| 8 | 117 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and |
| 118 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. | |
|
11
59054f086eca
Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents:
10
diff
changeset
|
119 Matthias Bernt (@bernt-matthias) added log and trimlog output. |
|
6
141bba0e9a77
Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents:
5
diff
changeset
|
120 |
| 1 | 121 Developers |
| 122 ========== | |
| 123 | |
| 124 This tool is developed on the following GitHub repository: | |
| 125 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic | |
| 126 | |
| 127 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 128 the ``package_trimmomatic.sh`` script. | |
| 129 | |
| 130 | |
| 131 Licence (MIT) | |
| 132 ============= | |
| 133 | |
| 134 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 135 of this software and associated documentation files (the "Software"), to deal | |
| 136 in the Software without restriction, including without limitation the rights | |
| 137 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 138 copies of the Software, and to permit persons to whom the Software is | |
| 139 furnished to do so, subject to the following conditions: | |
| 140 | |
| 141 The above copyright notice and this permission notice shall be included in | |
| 142 all copies or substantial portions of the Software. | |
| 143 | |
| 144 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 145 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 146 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 147 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 148 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 149 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 150 THE SOFTWARE. |