annotate README.rst @ 15:32f1f56bd970 draft

Updated for Trimmomatic 0.39 and adds quality score options.

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 care of installing the tool wrapper
and the trimmomatic program and data, and setting the appropriate environment
variables.

Controlling the available memory
================================

The default amount of memory avilable to trimmomatic is set to 8GB.
To change the default amount of memory you can set the environment variable
``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
set this is in the job_conf.xml file. To change the available memory to 6GB, a
line like the below should be added:

``<env id="_JAVA_OPTIONS">-Xmx6G</env>``

This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.

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:

    <tool file="trimmomatic/trimmomatic.xml" />

You will also need to install trimmomatic 0.38:

- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.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-0.36.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
---------- ----------------------------------------------------------------------
0.39       - Update to Trimmomatic 0.39.
0.38.1     - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is
             supported across both Linux and MacOS platforms.
0.38.0     - Update to Trimmomatic 0.38.
0.36.6     - Added trimlog and log outputs; add support for ``fastqillumina``
             and ``fastqsolexa`` input types
0.36.5     - Remove tool_dependencies.xml and always use conda to resolve tool
             dependencies
0.36.4     - Add option to provide custom adapter sequences for ILLUMINACLIP
           - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP
             in palindrome mode
0.36.3     - Fix naming of output collections. Instead of all outputs being called
             "Trimmomatic on collection NN" these will now be called "Trimmomatic
             on collection NN: paired" or "Trimmomatic on collection NN: unpaired".
0.36.2     - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input
             the output will also be fastqsanger.gz.
           - Use $_JAVA_OPTIONS to customize memory requirements.
0.36.1     - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version
             is still supported for now).
0.36.0     - Update to Trimmomatic 0.36.
0.32.4     - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
0.32.3     - Add support for FASTQ R1/R2 pairs using dataset collections (input
             can be dataset collection, in which case tool also outputs dataset
	     collections) and improve order and naming of output files.
0.32.2     - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
             at runtime (default is 6).
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 <command> 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
========== ======================================================================


Credits
=======

This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs).
Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 
support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP.
Matthias Bernt (@bernt-matthias) added log and trimlog output.
Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
support across Linux and MacOS.
Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.

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)
=============

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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.

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