Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: galaxy.web.framework.decorators ERROR 2022-11-04 13:22:12,200 [pN:main,p:68269,tN:WSGI_0] Uncaught exception in exposed API method:
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: Traceback (most recent call last):
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: File "/srv/toolshed/test/server/lib/galaxy/web/framework/decorators.py", line 337, in decorator
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: rval = func(self, trans, *args, **kwargs)
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: File "/srv/toolshed/test/server/lib/tool_shed/webapp/api/repositories.py", line 366, in index
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: shed, _, owner, name, tool, version = tool_id.split("/")
Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: ValueError: not enough values to unpack (expected 6, got 1)
Sorry the owner is dave
great
Good job!
I'm adding another worker, so the testoolshed will be down for a couple of minutes
alright, it's back. if someone wants to try repo creation and update that would be nice
haha, ok, this isn't urgent, but I won't get around to doing it next week
Hold onto that thought! I'm working on ripping all the client code out of the main build and expect to break it again soon.
(the toolshed)
I am currently facing the following issue: I have a tool (https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy2) that expects a multi-sequence FASTA file and, in my case, a list of PE data (representing different samples. The tool will then find the fasta sequence that best matches the reads in each input and will produce a results collection equal in number of elements to the number of PE input samples.
So far, so good.
Now, however, I would like to extend this to a collection of multisequence fastas, and I want a run of each sample against each such fasta resulting in a nested list with e.g. samples as the elements of the outer list and assigned best match for that sample for each of the multi-sequence Fastas.
So far, so good.
Now, however, I would like to extend this to a collection of multisequence fastas, and I want a run of each sample against each such fasta resulting in a nested list with e.g. samples as the elements of the outer list and assigned best match for that sample for each of the multi-sequence Fastas.
After many attempts I'm about to conclude that there's no elegant way to achieve this, but maybe I'm wrong?
The only rather stupid-looking solution I have is to extract, as part of a workflow, each multi-sequence fasta (it's always eight of them) with
__EXTRACT_DATASET__, then run vapor on each of those datasets and the list:paired collection.
I can live with that if it's the only way, but don't want to build something dumb.
So instead of lining up collections to be processed match by match you want to do all possible combinations?
IIRC we do support that in the backend, but haven't enabled this for lack of a user interface. Just to be sure, can you share a history with your workaround ? I wonder if this could also be done by nesting your collection deeper
https://usegalaxy.eu/u/wolfgang-maier/h/vapor-nested-attempts
Collections 11 and 15 are the relevant inputs.
Collections 11 and 15 are the relevant inputs.
hey workflow gurus! staramr specifies species using a drop down (this is necessary to run PointFinder) - while the user could set this by changing the "default tool parameters" at pipeline invocation time, is there any way to ask for a user input parameter for the pipeline (so it shows up right at the top like other pipeline inputs) and connect this to the dropdown?
Yes, you can click on the
add connection to module button, then connect a text parameter to that input
It'll be shown as a select list
Note that only works for selects, not conditionals, since conditionals can add arbitrary inputs and outputs, breaking workflows
ah damn, the staramr input is a conditional - instead of making it "use pointfinder: yes / no" and then "which database", they (PHAC-NML) combined it into one
I think this particular conditional could be flattened by moving the unvalidated one into the main select, then checking whether or not the custom flag is needed in cheetah
The next workflows call is in 60 minutes:
Workflow WG call
Thursday, 17 November · 16:00 – 17:00
Google Meet joining info
Video call link: https://meet.google.com/myu-vozy-bsj
Workflow WG call
Thursday, 17 November · 16:00 – 17:00
Google Meet joining info
Video call link: https://meet.google.com/myu-vozy-bsj
Sounds like there's some movement on the workflowhub side, but will do!
I think I got most of the backend modalities worked out for conditional steps, if you want to have a look at the test case and assumptions, they're in lib/galaxy_test/api/test_workflows.py here: https://github.com/galaxyproject/galaxy/pull/14846/files#diff-62218e13fbfad227cca222eb36d1801285ceb01eb2f9eb0c14aa99175bddd762R1896 ... no UI yet, that's the next thing I'll work on