Installation

After installing the export_to_cluster tool, you need to setup an environment variable to specify the directory where users are expected to save their files. One way to do that is:

1. create a directory called EXPORT_DIR_PREFIX in your tool dependencies directory (which by default is database/dependencies/, but can be changed in your Galaxy config file)

2. in this directory, create a file called env.sh with a content similar to the following template:

   EXPORT_DIR_PREFIX=/PATH/WHERE/TO/SAVE/FILES; export EXPORT_DIR_PREFIX
   

3. create a symlink called default inside the EXPORT_DIR_PREFIX directory pointing to the same directory, e.g.:

   $ cd TOOL_DEPENDENCIES_DIR/EXPORT_DIR_PREFIX/
   $ ln -s . default
   

Alternatively, you could define the EXPORT_DIR_PREFIX environment variable in your config/job_conf.xml file for the destination where the export_to_cluster tool is going to run (for an example, see _JAVA_OPTIONS in config/job_conf.xml.sample_advanced), but this would define the environment variable also for all the other tools that use that destination (normally not a problem, but worth to mention).