I'm trying to make sense of how to use
planemo autoupdate - if I just run it locally it times out trying to install tools... so I'd like to use the --profile option... but I don't understand how profiles work... they seem to need a Galaxy URL and Galaxy user or admin API key... but I don't see where the Galaxy user is specified. Or what the database stuff is for
With the API key you don't need to specify a user. Galaxy will know which user belongs to the API key.
Hey @pvanheus I don't think you need to use a profile. It should be enough to append
--galaxy_url URL --galaxy_user_key API_KEY to the command
and do I need to tell it to use the external_galaxy engine?
But it will probably be a lot faster to point it towards a server, since you can skip tool installation
but then you can only update the workflow to at most the latest version of the tools which are installed on that server
Are you reading the planemo documentation atm or something else? Maybe I can write a few lines extra explanation
planemo documentation... this section: https://planemo.readthedocs.io/en/latest/autoupdate.html#updating-workflows
so I tried
planemo autoupdate --galaxy_url http://blah --galaxy_user_key blah workflow.ga with planemo 0.74.9 and it doesn't recognise the galaxy_url flag
I was wrong, it seems you have to use a profile. Probably that should be changed since it seems people generally prefer to enter URL and API key directly
planemo profile_create my_new_profile --galaxy_url http://blah --galaxy_user_key
and then
planemo autoupdate workflow.ga --profile my_new_profile
seems it doesn't work with a 21.01 server
Hi, can someone else review this PR : galaxyproject/tools-iuc#4560 in order to merge it ? Thank you !!
Do we any new policy for specifying tool onthology within the wrapper in order to feel the new tool panel?
You can use:
<xrefs>
<xref type="bio.tools">orfipy</xref>
</xrefs>which will point to https://bio.tools/orfipy
and should we thus be adding them for every tool?
they're used for fetching the edam terms, which are then used to make the nice edam based categories in the alternative views of the panel
definitely please add them :)
If the tool is on https://bio.tools/ , IUC recommends to add a
bio.tools xref, which should provide the EDAM ontology xrefs automagically.
Hope all is ok on your sides
We are looking at creating tools who need to take as input couples of datafile and related metadata file, and this is manage for now using file names. I don't find good info / doc on how t omanage input data file names and so on so we can be sure to have ths good "links" between data and related metadata if users select multiple files as input....
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https://github.blog/2022-05-09-supercharging-github-actions-with-job-summaries/ maybe would be nice for tool testing reports, we could have more detail directly visible and not requiring download
hey there... for our IRIDA deploys we need to have Singularity images - on Galaxy servers these are either (1) pulled from quay.io using the
mulled_singularity resolver or (2) (for non-IUC tools) built using the build_mulled_singularity resolver (which actually doesn't work for me at the moment). how can this functionality be run on the command line or via API so that I can get the Singularity images for IUC tools (or potentially for non IUC tools) without running things through a Galaxy server?
planemo mull tool_path. If these are to be built for galaxy tools you can register your tools in https://github.com/galaxyproject/planemo-monitor
the build_mulled_singularity resolver works and has tests
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singularity itself can convert docker images to singularity images, no CLI needed
Can I get a merge on galaxyproject/tools-iuc#4564 ? I think we'll need this to run the tests against 22.05 in the release testing process
Would the iuc welcome wrappers for seqkit (https://bioinf.shenwei.me/seqkit/) tools? I've got a lab that needs some of them, but hoping for feedback since there are several other existing tools that perform similar tasks. Thanks in advance!
Looked at it half a year ago or so, but had no time to do any wrapping work on it. Quite some overlap with tools we have already, but always good to have alternatives :)
More details on that are in https://planemo.readthedocs.io/en/latest/writing_advanced.html#processing-identifiers
Yes that'll work. You probably want to escape some characters as with the regex mentioned in the docs
so...
planemo mull uses involucro to build a Docker contain on the local machine... and singularity build can pull from a Docker registry to build a Singularity image. is there a way to avoid round-tripping through a Docker registry when building Singularity images?
2 replies
@sncgbrl
Hello everyone, I am trying to upload my data but I am getting this #error
(Warning: Error: tus: unexpected response while creating upload, originated from request (method: POST, url: /api/upload/resumable_upload/, response code: 502, response text:
Galaxy
Galaxy could not be reached
You are seeing this message because a request to Galaxy timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please check for additional information on the Galaxy status page or the @galaxyproject Twitter feed. If the issue is not addressed on those sources, you may report it to the support team at galaxy-bugs@galaxyproject.org with details on what you were trying to do and the URL in the address bar.
, request id: n/a)
Can anyone explain to me what is the problem ?
thank you very much in advance.
1 reply
I could produce an interleaved file, subsample with seqtk, then deinterlace ... but that seems more complicated than necessary