Hi Denise,
Although the instructions you found can still be used, a couple of steps
can be updated now so I'll to that now and hopefully answer your questions
in the process.
Updated instructions:
1. Start a brand new Galaxy CloudMan cluster/instance (this will be only a
temporary cluster needed
I am not aware of any other way new_file_path is accessed. Is it old
jobs that were queued up prior to the switch? I think
job_working_directory might actually be affected by the settings in
your object store configuration. Have you configured an object store?
In either case - knowing the
Can you review this dev thread
http://dev.list.galaxyproject.org/Problem-selecting-datasets-with-a-specified-datatype-td4665366.html?
In particular can you go to the View data types registry option in
the admin menu and see if Galaxy thinks it knows about this datatype?
Let me know if Galaxy
I think a working example that uses this pattern is Bjoern's glimmer tool:
https://github.com/bgruening/galaxytools/tree/master/glimmer3
The only obvious difference I see that he sets the environment
variable to $REPOSITORY_INSTALL_DIR in tool_dependencies.xml
(environment_variable
It looks like this was a problem for awhile but isn't anymore on main
https://trello.com/c/yFeXvhUg.
It doesn't look like there has been any changes to the bowtie2 wrapper
since it was migrated to the tool shed so I am not sure why it isn't
working for you?
As an admin can you open a successful
Hello Liz,
I wish I had some better news - upgrading might help - we have
definitely made modifications to that file since then - but not to
address this issue I don't think. What would be really interesting is
to see the Galaxy logs around the time of that error - I wonder if
there would be
Dear Galaxy-Dev,
Last week I downloaded a fresh version of Galaxy with all stable updates. I've
just come across a NameError in the upload.py tool.
Traceback (most recent call last):
File /home/rob/galaxy-dist/tools/data_source/upload.py, line 390, in
module
__main__()
File
