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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
pvanheus
@pvanheus
ok then that tool looks good
Björn Grüning
@bgruening
Hi @KyleL1998
If CRISPR Studio is just for CRISPRDetect we would need CRISPRDetect in Galaxy as well isn't it?
Is it already in Galaxy?
KyleL1998
@KyleL1998
I'm fairly certain its just for CRISPR Detect. I checked and can only find its github repo, it's not on galaxy and it can't be installed through conda. Yes you probably would this was a weird request then to skip past detect and go right for studio hum. @bgruening.
M Bernt
@bernt-matthias
Morning everybody. I tried to test with cached reference data here: galaxyproject/tools-iuc#2368 .. but the tests are failing. If I uncomment the filter and validator they are successful. I also tried to add a dbkey="test" to the iput files, but this also does not help.
Alex Ostrovsky
@astrovsky01
Hi everybody! I just started working with Galaxy and will be working on wrapping tools for the next few months. I was hoping you all could give me advice on how you all go about identifying tools to wrap or your process for going about doing so? Thank you!
M Bernt
@bernt-matthias
Hi @astrovsky01: I create new wrappers usually if users at our research institute ask for them. Besides new wrappers I often update tools (new versions / missing options) if I discover such a thing. I guess that the IUC has an issue open somewhere listing missing tools.
Alex Ostrovsky
@astrovsky01
@bernt-matthias thank you! I'm looking through the repos now.
pvanheus
@pvanheus
@dfornika have you seen the discussion on the micro Slack about kraken2 databases? Do you think it is better to add to your kraken2 data manager or write a new kraken2-download data manager to import this work into Galaxy (and thus IDC)?
secondly I notice you kraken2 data manager references a URL path in tools-iuc that doesn't exist. Is this a mistake or future planning?
Dave B.
@davebx
could I get a pair of eyes on galaxyproject/tools-iuc#2323?
pvanheus
@pvanheus
@davebx looks good.
Dan Fornika
@dfornika
@pvanheus I haven't seen that discussion you mentioned. I've been trying to set aside some time to finish up the data manager. I worked through some suggestions from @wm75 but haven't completed one of the larger suggestions which was to merge a few of the separate data managers into one.
pvanheus
@pvanheus
ok. that suggestion does make sense. I've tagged you into the other discussion.
so are you planning to PR it to tool-iuc when you're done?
Dan Fornika
@dfornika
I've got a work-in-progress pull-request here: galaxyproject/tools-iuc#2340
Dan Fornika
@dfornika
@pvanheus I've taken a quick look at CVMFS but otherwise I don't quite understand how the IDC project works. I think I'd like to focus on completing the existing data manager(s) and have them incorporated into tools-iuc. Would that cause any problems for the IDC option?
pvanheus
@pvanheus
no it can only help. thanks
Alex Ostrovsky
@astrovsky01
Hey everyone, I’m working on adding a python package called scvis, a parametric equivalent to tsne, to the toolshed. Right now, I’m working on writing the wrapper for some of the functions, but how would I go about adding the package itself?
Marius van den Beek
@mvdbeek
@astrovsky01 you just need to create a bioconda package, there are instructions here
once you have this you add a <requirement type="package" version="someversion">scivis</requirement> to your requirements section and Galaxy will know how to get the package
Alex Ostrovsky
@astrovsky01
@mvdbeek awesome, thank you!
Marius van den Beek
@mvdbeek
no problem, let us know if you're having issues
Jennifer Hillman-Jackson
@jennaj
@dfornika Hi! A user is having problems with the Kraken2 DM in the test tool shed. Do you have any advice to help them with usage .. or are there known issues? https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/5
Dan Fornika
@dfornika
Hi @jennaj, thanks for getting in touch. As you mentioned in your comment on the help site, that tool was only uploaded to the test toolshed for testing/development and isn't intended for general use. I'll reply on the help site with more detail.
M Bernt
@bernt-matthias

Struggling with the integration of FastQC and MultiQC in a workflow for paired data.

  • if I start with a pair -> FastQC -> flatten collection -> MultiQC I get only 2 entries in the MultiQC report since in the FastQC raw all data sets are named forward or reverse, resp.
  • the idea to start with a collection -> unzip -> aplly FastQC on the forward and reverse collection -> feed them separately to MultiQC does not work since the collections are not connenctable to FastQC

Any suggestion for a solution or for possible changes to the wrappers?

See also galaxyproject/tools-iuc#2371
Marius van den Beek
@mvdbeek
Yeah, so if you're okay with having dangling _r1/_r2 names in the overview you can flip the input type to list:paired in multiqc and do the magic there
IMO this makes it hard to read if you have more than a handful of samples, but if you implement this I would have no problem merging it
Half the work is already done in https://github.com/galaxyproject/tools-iuc/pull/2028/files, you just have to do it for the forward strand read as well
M Bernt
@bernt-matthias
Thanks @mvdbeek .. will have a look
Does someone has experience with <assert_command> + <has_text>. To me it seems that this does not work at all. But maybe I'm doing something wrong.. would be nice if someone could have a look here: galaxyproject/galaxy#7730
Alex Ostrovsky
@astrovsky01
Update for anyone working with tools that use Tensorflow. Bioconda is currently having issues with builds that include it.
bioconda/bioconda-recipes#14499
M Bernt
@bernt-matthias
Question regarding embeding images in help: I use .. image:: $PATH_TO_IMAGES/pairpipe.png and have placed the image at static/images/pairpipe.png . With planemo s I do not see the image (I see a 404 in the browsers debug console). Is this a limitation of planemo, or am I doing something wrong?
Marius van den Beek
@mvdbeek
it's a limitation of the framework
$PATH_TO_IMAGES is ignored, we just look up the image in static/images
https://github.com/galaxyproject/galaxy/blob/dc1834c93b33b1b30747d4e76e1998d34f986140/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py#L253
we should really fix this, this is a very old issue
Marius van den Beek
@mvdbeek
(I mean the local display, if you install via the toolshed it'll work fine)
M Bernt
@bernt-matthias
OK. Thanks for the information.
Alex Ostrovsky
@astrovsky01
Having created a dependency for a tool via bioconda, how do I call it from there in my galaxy toolshed? I wrote my xml, and now the documentation says to add the tool file, but the only .py I have is the setup file.
Devon Ryan
@dpryan79
Is the tool itself in bioconda or just one of its dependencies? That is, are you trying to install a "local tool"?
Alex Ostrovsky
@astrovsky01
I put the whole tool there. In fact, to test it, the tool version I'm running right now is the one I pulled from there.
Devon Ryan
@dpryan79
There's usually not a tool file then. You just add a requirements section (e.g., https://github.com/deeptools/deepTools/blob/master/galaxy/wrapper/deepTools_macros.xml#L6-L9 )
Alex Ostrovsky
@astrovsky01
I think it may be an issue with my xml file then. By the error, I wasn't sure. Thank you!
Devon Ryan
@dpryan79
Good luck!
Alex Ostrovsky
@astrovsky01
@dpryan79 the error seems to be with Galaxy's ability to actually read the tool from the path. I tried making the most basic .xml file I could, with just a command of echo that took an input file and printed an unrelated statement just to test after I couldn't find the line making the error. Here is the log:
galaxy.tools.toolbox.base ERROR 2019-04-30 11:06:36,684 [p:5445,w:0,m:0] [MainThread] Error reading tool from path: myTools/scvis.xml
Traceback (most recent call last):
File "lib/galaxy/tools/toolbox/base.py", line 570, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False)
File "lib/galaxy/tools/toolbox/base.py", line 755, in load_tool
tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds)
File "lib/galaxy/tools/init.py", line 271, in create_tool
raise e
M Bernt
@bernt-matthias
I would suggest to use planemo for testing and developing. With planemo s or planemo t you can serve or test a tool
Devon Ryan
@dpryan79
I strongly second @bernt-matthias's suggestion. planemo is about the best thing since sliced bread when it comes to galaxy tool development.