This is a module for Galaxy that allows to run Discrover.

How to use it

In the instructions below, we designate two paths by shell variables: $P stands for the path where you clone the Discrover Galaxy module's source code into, and $GALAXY_PATH is the main directory of the source code of your Galaxy instance.

0. Install Discrover.

1. Install an instance of Galaxy, following these directions.

2. Clone this repository into the main directory of your galaxy instance:

   cd /some/place/for/the/Discrover/Galaxy/module/source/code
   export P=`pwd`
   git clone git@github.com:maaskola/discrover-galaxy.git

3. Add a symbolic link:

   cd $GALAXY_PATH/tools
   ln -s $P/discrover-galaxy/tools/discrover discrover

4. Modify tool_conf.xml in the main directory of the Galaxy instance to include a section for this module. Find the section with 'id' equal to 'motifs' (around line 132) and add a line

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

into it, such that it looks something like this:

```xml
<section id="motifs" name="Motif Tools">
  <tool file="meme/meme.xml" />
  <tool file="meme/fimo.xml" />
  <tool file="discrover/discrover.xml" />
</section>
```

5. Start your Galaxy instance by executing cd $GALAXY_PATH && ./run.sh. Fire up a web browser and go to http://localhost:8080. The Discrover module is available in the left-side pane under the section 'Motif Tools'.