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Uploaded fix from Marius van den Beek (make readlink more portable)

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 0.36:

- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.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
---------- ----------------------------------------------------------------------
0.36.6     - 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.

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.