Mercurial > repos > earlhaminst > export_to_cluster
diff README.rst @ 3:9838eed606ad draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
author | earlhaminst |
---|---|
date | Wed, 09 May 2018 05:52:40 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed May 09 05:52:40 2018 -0400 @@ -0,0 +1,17 @@ +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). +