Dear Evan,
you need to setup an environment variable for the tool 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/` )
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 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).
Cheers,
Nicola
On 05/05/18 15:04, Evan Clark wrote:
Have you ever seen this error with export to cluster?
export_to_cluster.py: error: Directory prefix cannot be empty
Nicola Soranzo wrote:
Hi Evan,
you can have a look at
https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/
<https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/b97775e9fe06>
Hope that helps!
Cheers,
Nicola
On 27/03/18 16:03, evan clark wrote:
Has anyone attempted to write a tool that allows copying of galaxy
datasets locally, i.e. without downloading via http. We have scenario
where there are some additional tools available only via command line
and it would be very useful to be able to directly copy galaxy
datasets from the datasets folder.
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