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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
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    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
Michelle Savage
@hujambo-dunia:matrix.org
[m]
Hello 👋 Does anyone know why we include the utils\localization.js file in 100+ of our VUE & JS Galaxy files? Is this necessary since there are only 3 files in the codebase where language can be changed by the user? (e.g. Home Page, Login Page, and Preferences Page)
3 replies
bgruening
@bgruening:matrix.org
[m]
Another new contributor that struggles with the test size limitation: galaxyproject/tools-iuc#4516
Any idea wat to do here?
M Bernt
@bernt-matthias

@bgruening:matrix.org for the particular usecase I was wondering if the ncbi taxonomy data table could be reused.

manual merge and deploy? if this happens more often it would be cool to have a way to disable size checks for certain paths .. maybe an additional file like .tt_skip

on the long run progress with galaxyproject/galaxy#13495 :)

was just wondering if we could use the data on the CVMFS for this case (use cached in the tool's conditional). But its kind of circular, since we would need the data manager or at least the datatable + data on CVMFS before accepting the tool. Also CI would need to be adapted to set the --tool_data_table parameter of planemo test

wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Would anyone have any insight into https://github.com/galaxyproject/tools-iuc/pull/4533#issuecomment-1114675492?
In particular, is there supposed to be any inherent difference in dependency management between a regular and a data manager tool?
Marius
@mvdbeek:matrix.org
[m]
As usual, a recent profile version would fix this
I'm writing a comment
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Thanks!
Marius
@mvdbeek:matrix.org
[m]
I'd totally appreciate a review/merge on galaxyproject/tools-iuc#4502
bgruening
@bgruening:matrix.org
[m]
on it
M Bernt
@bernt-matthias:matrix.org
[m]

Just checked recent weekly CI errors. Seems that samtools sort output may depend on the number of used CPUs (sorting is correct, just the order of alignments with the same mapping position may differ). Wondering how to deal with this ..

Just check for the number of lines and maybe some regex (does this work for bam?)?

M Bernt
@bernt-matthias
Currently looking at bowtie2 ... Maybe we just implement https://github.com/samtools/samtools/issues/891#issuecomment-404229654 .. mapper | samtools sort -@2 ... | samtools -@\$GALAXY_SLOTS .. which also solves the problem the parallel sorting and mapping may use to many CPUs
M Bernt
@bernt-matthias
i.e. use a fixed number of cores (1) for sorting and all cores for compressing to bam
Jory Schossau
@JorySchossau
Hi, I'm curious if anyone here could comment on if making a Galaxy Tool would be appropriate for our project? I'm assessing the best way to disseminate our multi-year project as a tool. The tool involves a small (<100) set of input sequences, then uses a combination of our method and a variety of published/vetted methods to produce unified predictions. If we optimize some code, we could get the runtimes down to perhaps less than a day. We can already make an offline tool, so our goal is about making use of better computer resources and a more open science workflow than just a user's laptop. Memory requirements are less than 32GB.
bgruening
@bgruening:matrix.org
[m]
Upps. Answered in the other chat.
But this one is the correct one.
Jory Schossau
@JorySchossau
Would you recommend I try to attend the upcoming Training Day or maybe CoFest if I'd like to learn/ramp up on Galaxy tool development?
bgruening
@bgruening:matrix.org
[m]
Always :)
But to be honest this training here is super cool and you will learn everything that is needed.
It will take you 6h and you know even the details.
We can help you then reviewing your tool before it gets uploaded to the ToolShed ...
Jory Schossau
@JorySchossau
@bgruening:matrix.org Thanks!
pvanheus
@pvanheus
hey there... I'm working on writing a data manager to manage pangolin's data assets. there are 3 of these - pangolin-data, constellations and pangolin-assignment - and they get updated on different schedules (although pangolin-data and pangolin-assignments try and stach in sync). so there are going to be 3 data tables. this is all for a single purpose though, so I'm wondering: make 3 DMs? or make 1 DM with options to update 3 tables? (i.e. either 1, 2 or all 3 tables)
pvanheus
@pvanheus
another DM question - how can the existing contents of the data table be queried? its not in the data table that gets passed to the DM. this was less of a concern for me before, but now I'm working on a DM that potentially could download 100s of MBs of data, and avoiding re-downloading what is already there would be useful.
pvanheus
@pvanheus
one can look inside $__app__ at tool_data_tables but this seems rather nasty....
pvanheus
@pvanheus
I'll note that I used $__app__.tool_data_tables in data_manager_primer_scheme_bedfiles, so I guess that's the way to go
M Bernt
@bernt-matthias
@pvanheus .. the best would be galaxyproject/galaxy#12941 .. unfortunately I did not find time to fix the tests .. and it will only be available from the nextr release
pvanheus
@pvanheus
thanks @bernt-matthias but that wouldn't fix this exact problem - in this case there's a list of releases (on Github) and then a user specifies a range (of dates or versions) that they want to capture... the DM then downloads the ones that are available but missing locally.
M Bernt
@bernt-matthias:matrix.org
[m]
Ah, OK. Fancy.. Then I think $__app__.tool_data_tables sounds reasonable
Gulsum Gudukbay Akbulut
@gulsumgudukbay
Hi everyone, I am working on adding GPU support for the local galaxy runner. Currently, the support is in the PR stage but once it is finished, we wanted to see how would GPU support affect the speed of research and how much the GPU-supported tools would be used.
To this end, I have two main questions:
  1. Which tools (that already have GPU support) are frequently used by researchers? (Currently, I know that racon was a popular one, any tool similar to this that could benefit researchers would be great).
  2. Which machine learning tools are popular among researchers and which domain researchers mainly use ML tools that are in Galaxy? (Asking this, because many ML tools can easily be GPU supported due to the usage of Python libraries)
bgruening
@bgruening:matrix.org
[m]
@gulsumgudukbay: you are searching for native GPU application or also tensorflow application?
1 reply
Hey everyone, this PR is a very good opportunity for a first-time contributor: galaxyproject/tools-iuc#4492
if you want to contribute this tool is easy to handle and needs an update
you need to add the missing parameters of the new version
Gulsum Gudukbay Akbulut
@gulsumgudukbay
@bgruening both would be fine. Any application that is used frequently is good for testing how beneficial the support is
Nate Coraor
@natefoo:matrix.org
[m]

I was trying to figure out why most of the tool tests of all versions of Pangolin 3.x fail on usegalaxy.org with:

AttributeError in line 112 of /usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk:
'DecisionTreeClassifier' object has no attribute 'n_features_'
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk", line 112, in __rule_pangolearn
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/pangolearn/pangolearn.py", line 170, in assign_lineage
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 922, in predict_proba
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 395, in _validate_X_predict
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message

Both conda and singularity, and so wanted to see how usegalaxy.eu had fixed it - turns out, it's broken on EU too.

This seems to imply it's an install issue but I suspect reinstalling the deps isn't going to help in this case: cov-lineages/pangolin#427
fwiw I also get the following with pangolin 4.0.5+galaxy1 on EU (I don't have 4.x on .org):
Error: the input query fasta could not be parsed.
Double check your query fasta and that compressed stdin was not passed.
Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions.

Error: the input query fasta could not be parsed.
Double check your query fasta and that compressed stdin was not passed.
Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions.
rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/out.3651279': No such file or directory
rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/err.3651279': No such file or directory
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
I've been trying to explain to them why it's not a great idea to switch your scikit-learn version when building models for a given release, but seems they rae not really getting the point :(
That's for your 3.1.20 question.
Older models installed via a DM are working still.
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Regarding the v4 series, there should be 4.0.5+galaxy2 in the toolshed already (not sure why it didn't get installed on .eu over the weekend), which addresses a few issues. Your error message really looks like something's wrong with your FASTA input though. If not, then what were the exact parameters you've been using?
Nate Coraor
@natefoo:matrix.org
[m]
I was running the tool tests using galaxy-tool-test
kenza12
@kenza12
Hi, I opened this PR to update rpbasicdesign tool : https://github.com/brsynth/tools-iuc/pull/new/rpbasicdesign_update_1_1_0 . Can anyone review/merge it please ? I also opened this PR (galaxyproject/tools-iuc#4458) for another tool (dnabot) and it was merged but I can't find it in the toolshed . Can you check what's wrong please? Thank you for your work.
Yvan Le Bras
@yvanlebras
Hi amazing IUC!
Hope all is ok on your sides !
We are trying to add some conda recipes but tests fails...
If someone has an idea conda-forge/staged-recipes#18967
1 reply
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
> library('dissUtils') 2022-05-17T07:43:35.5948057Z Error in library("dissUtils") : there is no package called 'dissUtils'