| Previous changeset 2:b97775e9fe06 (2017-03-24) |
|
Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5 |
|
modified:
export_to_cluster.py export_to_cluster.xml |
|
added:
README.rst |
| b |
| diff -r b97775e9fe06 -r 9838eed606ad README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed May 09 05:52:40 2018 -0400 |
| b |
| @@ -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). + |
| b |
| diff -r b97775e9fe06 -r 9838eed606ad export_to_cluster.py --- a/export_to_cluster.py Fri Mar 24 12:20:48 2017 -0400 +++ b/export_to_cluster.py Wed May 09 05:52:40 2018 -0400 |
| [ |
| @@ -24,11 +24,11 @@ real_export_dir = os.path.realpath(options.export_dir) dir_prefix = options.dir_prefix.rstrip(os.sep) if not real_export_dir.startswith(dir_prefix): - raise Exception("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix)) + raise Exception("'%s' must be a subdirectory of '%s'" % (options.export_dir, dir_prefix)) if not os.path.exists(real_export_dir): - raise Exception("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir) + raise Exception("'%s' directory does not exist or it is not accessible by the Galaxy user" % options.export_dir) if not os.path.isdir(real_export_dir): - raise Exception("%s is not a directory" % options.export_dir) + raise Exception("'%s' is not a directory" % options.export_dir) dataset_paths = args[::3] dataset_names = args[1::3] |
| b |
| diff -r b97775e9fe06 -r 9838eed606ad export_to_cluster.xml --- a/export_to_cluster.xml Fri Mar 24 12:20:48 2017 -0400 +++ b/export_to_cluster.xml Wed May 09 05:52:40 2018 -0400 |
| [ |
| @@ -1,16 +1,14 @@ -<tool id="export_to_cluster" name="Export datasets to cluster" version="0.0.1"> +<tool id="export_to_cluster" name="Export datasets to cluster" version="0.0.2"> <requirements> <requirement type="set_environment">EXPORT_DIR_PREFIX</requirement> </requirements> - <command detect_errors="aggressive"> -<![CDATA[ + <command detect_errors="aggressive"><![CDATA[ python '$__tool_directory__/export_to_cluster.py' -d '$export_dir' -p "\$EXPORT_DIR_PREFIX" #for $d in $datasets - '${d}' '${d.hid}: ${d.name}' '${d.ext}' + '${d}' '${d.hid}: ${d.element_identifier}' '${d.ext}' #end for > '$log' -]]> - </command> + ]]></command> <inputs> <param name="datasets" type="data" format="data" multiple="true" label="Datasets to export" /> <param name="export_dir" type="text" value="" label="Directory where to export the datasets" help="Must be writable by the Galaxy user"> @@ -23,8 +21,8 @@ </outputs> <tests> </tests> - <help> + <help><![CDATA[ Simple tool to copy datasets to a directory on the cluster. - </help> + ]]></help> <citations/> </tool> |