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Daniel Blankenberg
@blankenberg
see the bottom, for the latest uwsgi version
Tomas
@TKlingstrom
@OskarSLU , I think I found a (or the?) commit related to the issue: galaxyproject/galaxy@107c89a
But I think @jmchilton or @dannon can help out as I spoke a bit with them about it in June.
Nicola Soranzo
@nsoranzo
@OskarSLU @TKlingstrom Maybe galaxyproject/galaxy#6559 is relevant
Tomas
@TKlingstrom
I think it is very relevant and that "people" in this case includes me =).
John Chilton
@jmchilton
It sounds like a problem on the backend if there are actual failures though - I don't really understand how that can be. I assume you are running Galaxy locally on your computer without a job manager?
Tomas
@TKlingstrom
We are running Galaksio (I work with @OskarSLU ).
Tomas
@TKlingstrom
Huge thanks btw for that addition.
Miriam Payá
@mpaya
Hello. I'm new to galaxy, used to work on the command line before. I'm trying to gather metrics from a dataset collection with concatenate (cat), but I'd like first to include the name of each dataset into the results - either add dataset_name as first column, or replace an useless string with sed 's/string/${dataset_name}/' -.I can't find a way to do this on the forum. Is it possible? Thank you.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
if you're the admin you can install https://toolshed.g2.bx.psu.edu/repository?repository_id=050cbba300e2dbed&changeset_revision=b31219f26a8f
(or maybe it is already installed on the server you're using)
Miriam Payá
@mpaya
wow thanks, looks perfect
Miriam Payá
@mpaya
I'm trying to run it but the files are of datatype txt. Is there a way to change it to tabular on all files, instead of going manually one by one?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
You can set the datatype at upload or force a datatype in the workflow editor, otherwise in the UI it is a bit annoying and you have to do it one by one at the moment
Miriam Payá
@mpaya
I'll have that in mind.
OskarSLU
@OskarSLU
@nsoranzo Yes that was it! Now it works like a charm! Thanks a lot!
Miriam Payá
@mpaya
I'm excited, it took quite long but I got the results. Thanks a lot!!
Ghost
@ghost~5772e7e2c2f0db084a206e1b
cool, glad it worked for you!
Martin Cech
@martenson
@mvdbeek damn, stop closing my valuable bug reports! With this speed I will soon be the #3 in the list of most complaining people.
pvanheus
@pvanheus
@nsoranzo I'm using conda 4.3.33 - installed by Galaxy - on ubuntu 16.04. The reports I can find of that bug report are from installations where virtualenv is in us but that isn't the case here
Nicola Soranzo
@nsoranzo
Mmh, don't know, never seen this one before, you could try to update to 4.4.10 and see if it still occurs
pvanheus
@pvanheus
@nsoranzo thanks for the suggestion, I will try
@nsoranzo 4.4.10 specifically or will 4.5.11 (which it is suggestion) be better?
pvanheus
@pvanheus
@nsoranzo ah! I think I have found the source of the error - the installation is hosted on a Windows NFS server... and now I see "CaseInsensitiveFileSystemError: Cannot extract package to a case-insensitive file system."
Jennifer Hillman-Jackson
@jennaj
Docker/SMTP config question at G Biostars -- does anyone recognize what the specific issue is? What additional info would help to troubleshoot? https://biostar.usegalaxy.org/p/29431/
galaxybot
@galaxybot
[gronke] So, I have a job that is paused. When I select "Resume Paused Jobs" it says "Your jobs have been resumed" but then the job is still paused. How do I fix this?
Jennifer Hillman-Jackson
@jennaj
This was reported last week but without an intact example. Is this at Galaxy Main https://usegalaxy.org?
If yes, please send an email to galaxy-bugs@lists.galaxyproject.org that includes a shared history link. Note the dataset numbers that include these paused jobs and please leave them undeleted.
galaxybot
@galaxybot
[jebediah_] hello
cwsr
@cwsr
Hello, I have encountered the following error when I was using nanopolish at galaxy uni Freiburg:

Fatal error: Exit code 2 ()

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

I have created .tar.gz file from a folder containing 4000 fast5 files on Mac OS
Could someone suggest any remedy to this problem? Thank you very much
galaxybot
@galaxybot
[gronke] jennaj sorry no, it wasn't. it was on our personal server. the job "pauses" and then the sam file becomes basically unusable.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
gronke: most of the pausing happens if one of the input files enters an unusable state, so you have to fix the input and then you can resume. We'll highlight which input that is in 18.09
Pierrick
@P.Lucas_gitlab
Hello, how to clean the data/tmp directory please? I use "cleanup_datasets.py" but only data/files is cleaned. Thanks for your answer.
Nicola Soranzo
@nsoranzo
@P.Lucas_gitlab I use a cron script which runs every day, the relevant part is:
tmpwatch --ctime 30d database/jobs_directory/
tmpwatch --ctime 14d -x database/tmp/upload_store database/tmp/
tmpwatch --ctime 3d database/tmp/upload_store/
Pierrick
@P.Lucas_gitlab
@nsoranzo thanks for your answer!
Pablo Moreno
@pcm32
Hi there! Can you run Galaxy against LSF without using DRMAA?
Nate Coraor
@natefoo
there's no plugin for it, you could use the condor runner as an example to write one, or use the cli runner and write an lsf plugin for the cli runner.
Pablo Moreno
@pcm32
Thanks Nate
What about pulsar, does it require as well DRMAA to talk to LSF, or does it have something to talk to LSF directly?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
it's the same infrastrcuture, so I'd assume yes
writing a cli runner is actually pretty straightforward, and despite the hackish nature I'm using the torque runner in production https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/util/cli/job/torque.py
Gildas Le Corguillé
@lecorguille
Still some issue with the "Share with a user", is anybody know why, as lambda user, we get this message in red: The histories you are sharing do not contain any datasets that can be accessed by the users with which you are sharing.. I have no difficulty as admin.
Nate Coraor
@natefoo
@pcm32: nope, its drmaa support is slightly different but for the cli it uses galaxy's plugins
Nate Coraor
@natefoo
i wrote some scripts to clean up file_path, if anyone might find them useful: https://gist.github.com/natefoo/b98a5f08cd62a6750cd1e338076e2cda
Tomas
@TKlingstrom
Is there any Tool for Json to tabular in Galaxy?
I found One for combining jsons which is nice but I am looking for One
Martin Cech
@martenson
you could probably use jq for it?