Importing CGAT scripts into galaxy

General Preparation

Add /ifs/devel/cgat to PYTHONPATH.

Make sure that extensions have been built:

python setup.py develop --multi-version

The following directories are important:

galaxy-dist

Location of the galaxy distribution

cgat-xml

CGAT directory within the galaxy distribution. Create by typing:

mkdir <galaxy-dist>/tools/cgat

cgat-scripts

The CGAT scripts directory.

Adding a script manually

The following instructions describe the steps necessary to add a cgat script to galaxy.

For example, we want to publish the bam2stats.py script. First, create a file in <galaxy-dist>/tools/cgat called bam2stats.xml with the following contents:

<tool id="bam2stats.py" name="Compute Stats from BAM file">
  <description>Compute stats for a bam file</description>
    <command
      interpreter="python">/ifs/devel/cgat/scripts/bam2stats.py -v 0 &lt; $input &gt; $output
    </command>
    <inputs>
       <param format="bam" name="input" type="data" label="Source file"/>
    </inputs>
    <outputs>
       <data format="tabular" name="output" />
    </outputs>
  <help>
  Compute statistics for a bam file.
  </help>
</tool>

Add an entry to tool_conf.xml for the script:

<section name="CGAT Tools" id="cgat_tools">
  <tool file="cgat/bam2stats.xml" />
</section>

After restarting galaxy, the bam2stats command should now be visible in the CGAT section.

Automatic conversion of scripts

The CGAT tool collection contains a script called <no title> that can create and xml file for inclusion into galaxy. To create a wrapper for Purpose, run:

python <cgat-scripts>cgat2rdf.py --format=galaxy <cgat-scripts>bam2stats.py > <cgat-xml>bam2stats.xml

As before, add an entry to tool_conf.xml for the script.

For automatted conversion, a few rules need to be followed (see below).

Writing galaxy compatible scripts

CGAT scripts have generally a call interface that is compatible with galaxy and can thus be easily integrated. However, to make automatic conversion as easy as possible, conforming to a few coding conventions help.

1. Assign a metavar type to command line options of genomic file formats. For example:

   parser.add_option("-b", "--bam-file", dest="bam_files", type="string", metavar="bam",
                     help="filename with read mapping"
                          " information. Multiple files can be "
                          " submitted in a comma-separated list"  )
   

2. Use Experiment.OptionParser instead of optparse.OptionParser. The former has some extensions that make creating galaxy xml files easier. In particular, Experiment.OptionParser permits supplying a list of ‘,’-separated values to options that accept multiple values.

3. Follow the CGAT script naming convention. If possible, scripts should be named <format_in>2<format_out>.py. Formats can be mapped to other types in <no title>. For example, stats and table are both mapped to the format tabular.