# HG changeset patch # User pjbriggs # Date 1418136093 18000 # Node ID 2bd7cdbb622860fbd888d01aec16cfccd1c13126 # Parent 3358c3d3014325c21ff92dd03200db4a5d5062c3 Add README and citation tags. diff -r 3358c3d30143 -r 2bd7cdbb6228 README.markdown --- a/README.markdown Mon Dec 01 10:40:07 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -Trimmomatic -=========== - -XML tool file and shell script wrapper for the Trimmomatic program, which provides -various functions for manipluating Illumina FASTQ files. - -Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university: - - * - -The reference for Trimmomatic is: - - * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a - user-friendly, integrated software solution for RNA-Seq-based transcriptomics. - Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7) - -Trimmomatic 0.32 can be obtained from: - - * - -The tool assumes that two environment variables have been set, in order to find the -appropriate files: - - * `TRIMMOMATIC_DIR` should point to the directory holding the - `trimmomatic-0.32.jar` file, and - - * `TRIMMOMATIC_ADAPTERS_DIR` should point to the directory holding the adapter - sequence files (used by the `ILLUMINACLIP` option). - -Both variables will be set automatically if installing the tool dependencies e.g. via -a toolshed; otherwise they will need to be set manually in the Galaxy environment. - -To add to Galaxy add the following to tool_conf.xml: - - - -(The tool no longer uses a `.loc` file to point to the location of the adapter -sequence files) - -### Changes ### - -0.32.1: Remove `trimmomatic_adapters.loc.sample` and hard-code adapter files into - the XML wrapper. - -0.32.0: Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and - (set the environment). Update tool versioning to use Trimmomatic version - number (i.e. `0.32`) with tool iteration appended (i.e. `.1`). - -0.0.4: Specify '-threads 6' in section. - -0.0.3 : Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. - -0.0.2: Updated ILLUMINACLIP option to use standard adapter sequences (requires the - trimmomatic_adapters.loc file; sample version is supplied) plus cosmetic - updates to wording and help text for some options. - -0.0.1: Initial version diff -r 3358c3d30143 -r 2bd7cdbb6228 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Dec 09 09:41:33 2014 -0500 @@ -0,0 +1,104 @@ +Trimmomatic: flexible read trimming tool for Illumina NGS data +============================================================== + +Galaxy tool wrapper for the Trimmomatic program, which provides various functions for +manipluating Illumina FASTQ files (both single and paired-end). + +Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university +http://www.usadellab.org/cms/index.php?page=trimmomatic + +The reference for Trimmomatic is: + +- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer + for Illumina Sequence Data. Bioinformatics, btu170. + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper and +the trimmomatic program and data, and setting the appropriate environment variables. + +Manual Installation +=================== + +There are two files to install: + +- ``trimmomatic.xml`` (the Galaxy tool definition) +- ``trimmomatic.sh`` (the shell script wrapper) + +The suggested location is in a ``tools/trimmomatic/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the line: + + + +You will also need to install trimmomatic 0.32: + +- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip + +The tool wrapper uses the following environment variables in order to find the +appropriate files: + +- ``TRIMMOMATIC_DIR`` should point to the directory holding the + ``trimmomatic-0.32.jar`` file +- ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter + sequence files (used by the ``ILLUMINACLIP`` option). + +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id trimmomatic + +You will need to have set the environment variables above. + +History +======= + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files + into the XML wrapper. +0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and + set the environment. + - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) + with tool iteration appended (i.e. ``.1``). +0.0.4 - Specify '-threads 6' in section. +0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. +0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires + the trimmomatic_adapters.loc file; sample version is supplied) plus + cosmetic updates to wording and help text for some options. +0.0.1 - Initial version +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_trimmomatic.sh`` script. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r 3358c3d30143 -r 2bd7cdbb6228 trimmomatic.xml --- a/trimmomatic.xml Mon Dec 01 10:40:07 2014 -0500 +++ b/trimmomatic.xml Tue Dec 09 09:41:33 2014 -0500 @@ -223,11 +223,18 @@ The reference for Trimmomatic is: - * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a - user-friendly, integrated software solution for RNA-Seq-based transcriptomics. - Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7) + * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer + for Illumina Sequence Data. Bioinformatics, btu170. Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you use it. + + + 10.1093/bioinformatics/btu170 +