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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Helena
@hexylena:matrix.org
[m]
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 :)
Nicola Soranzo
@nsoranzo:matrix.org
[m]
If the tool is on https://bio.tools/ , IUC recommends to add a bio.tools xref, which should provide the EDAM ontology xrefs automagically.
Yvan Le Bras
@yvanlebras
Hi everyone,
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....
4 replies
Helena
@hexylena:matrix.org
[m]
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
Marius
@mvdbeek:matrix.org
[m]
I assume there's more to it ?
pvanheus
@pvanheus
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?
Marius
@mvdbeek:matrix.org
[m]
planemo can build the docker images
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
1 reply
singularity itself can convert docker images to singularity images, no CLI needed
Marius
@mvdbeek:matrix.org
[m]
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
Greg Von Kuster
@gregvonkuster
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!
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
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 :)
Marius
@mvdbeek:matrix.org
[m]
Yes that'll work. You probably want to escape some characters as with the regex mentioned in the docs
pvanheusden
@pvanheusden:matrix.org
[m]
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
@sncgbrl

@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
Marius
@mvdbeek:matrix.org
[m]
Anyone know a tool that subsamples PE reads ?
I could produce an interleaved file, subsample with seqtk, then deinterlace ... but that seems more complicated than necessary
pvanheusden
@pvanheusden:matrix.org
[m]
I'm having a problem with my Galaxy run in galaxy serve - I use a local copy of the code and get this error - https://gist.github.com/pvanheus/986a1419d78012448a64a920c0a0df1f - its failing to parse a registry.xml file that is in the job working directory but I don't see where this fie is coming from? (it seems to contain datatypes_conf.xml and more)
2 replies
pvanheusden
@pvanheusden:matrix.org
[m]
I'm trying it again without --galaxy_root to see what happens. waaaaaiting for JS to compile.
Marius
@mvdbeek:matrix.org
[m]
Oh, martenson also reported this. I think we're going to disable TS datatypes by default in 22.05
I'll have another look if I can figure out how that can happen
martenson
@martenson:matrix.org
[m]
pvanheusden: seem similar to what I saw, the registry.xml is supposed to be there but mine was invalid with the actual datatypes configuration copied over many times
creating invalid xml
pvanheusden
@pvanheusden:matrix.org
[m]
martenson sounds exactly right. how did you fix it?
martenson
@martenson:matrix.org
[m]
Tried a couple of things, including changing release, and eventually it went away.
But I really do not know why it happened or why it went away
Sorry to not be of help
pvanheusden
@pvanheusden:matrix.org
[m]
LOL ok. so I seem to not have it if I don't use --galaxy_root
martenson
@martenson:matrix.org
[m]
check for some forgotten galaxy/gunicorn processes
It looks a bit like the file was written by multiple writers or so.
pvanheusden
@pvanheusden:matrix.org
[m]
yep. and I can't seem to find a cached version of the file anywhere.
martenson
@martenson:matrix.org
[m]
but it wasn't mangled, just some sections copied over and over
pvanheusden
@pvanheusden:matrix.org
[m]
mine had a <sniffer>...</sniffer></datatypes><datatype> in it - so bad XML
martenson
@martenson:matrix.org
[m]
mine was invalid xml for sure too, what I meant is that it was a bit too organized for a rogue writer theory
pvanheusden
@pvanheusden:matrix.org
[m]
yes, agreed.
Yvan Le Bras
@yvanlebras
Hi everyone
hope all is ok on your sides !
Just see that we have an issue trying to manage a binary file (with datatype not known from Galaxy) in our cheetah code on the XML tool file.... it seems that Galaxy ""don't see"" the file so we can't copy or use it
If we change the input datatype from "binary" to "binary,txt" and that we provide a txt file, "Galaxy see" the file (on the command line generated by Galaxy, we see the file name)
bgruening
@bgruening:matrix.org
[m]
do you have some code?
what does mean "not see"? in the UI?
Yvan Le Bras
@yvanlebras
no
;) sorry for the not precise questoin ;)
in the command line (when with planemo we execute the tool, then look at the job "information" and the "command line"), we have "nothing" where we put the $input (name of the input parameter)
when the file is binary