diff README.markdown @ 0:3358c3d30143 draft

Uploaded initial version.

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+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:
+
+ * <http://www.usadellab.org/cms/index.php?page=trimmomatic>
+
+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:
+
+ * <http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip>
+
+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:
+
+    <tool file="trimmomatic/trimmomatic.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 <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