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
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:
This will set the environment variable _JAVA_OPTIONS to -Xmx6G.
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:
The tool wrapper uses the following environment variables in order to find the
- TRIMMOMATIC_DIR should point to the directory holding the
- 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.
- Added trimlog and log outputs; add support for fastqillumina
and fastqsolexa input types
- Remove tool_dependencies.xml and always use conda to resolve tool
- Add option to provide custom adapter sequences for ILLUMINACLIP
- Add options minAdapterLength and keepBothReads for ILLUMINACLIP
in palindrome mode
- 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".
- 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.
- Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version
is still supported for now).
- Update to Trimmomatic 0.36.
- Add support for AVGQUAL and MAXINFO operations.
- 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.
- Use GALAXY_SLOTS to set the appropriate number of threads to use
at runtime (default is 6).
- Remove trimmomatic_adapters.loc.sample and hard-code adapter files
into the XML wrapper.
- 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).
- Specify '-threads 6' in <command> section.
- Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
- 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.
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.
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