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  • Jan 31 2019 22:04
    foellmelanie closed #336
  • Jan 31 2019 22:04
    foellmelanie opened #340
  • Jan 31 2019 13:58
    Maux82 commented #338
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    Maux82 commented #338
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  • Jan 30 2019 18:12
    bgruening commented #338
  • Jan 30 2019 10:24

    bgruening on tmgowan-flashlfq

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  • Jan 30 2019 10:24
    bgruening commented #339
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  • Jan 30 2019 10:24

    bgruening on master

    Modify for new FlashLFQ release… new test data for new version Merge pull request #339 from ga… (compare)

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    tmcgowan review_requested #339
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  • Jan 28 2019 20:45

    tmcgowan on tmgowan-flashlfq

    Modify for new FlashLFQ release… new test data for new version (compare)

  • Jan 28 2019 14:56
    bgruening commented #338
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  • Jan 23 2019 06:38

    bgruening on unipept4.0

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  • Jan 23 2019 01:47

    jj-umn on master

    unipept version 4.0 Currently … unipept.py - best_match of tryp… Remove extraneous text and 2 more (compare)

Pratik Jagtap
@pratikomics_twitter
Multiomics BOF at 12:15 PM at France Room for whoever is at GCC 2019
Björn Grüning
@bgruening
@caleb-easterly we got a request to get this into EU
you have a wrapper I have seen, do you want to PR this to GalaxyP?
Björn Grüning
@bgruening
Hi all! Can anyone help reviewing galaxyproteomics/tools-galaxyp#405 ?
Praveen Kumar
@pravs3683
@bgruening Hi Bjorn, can you please install msms_extractor on the usegalaxy.eu and proteomics.usegalaxy.eu. Thanks
M Bernt
@bernt-matthias
I'm just about to add some datatypes required for OpenMS: galaxyproject/galaxy#8109. Comments and wishes are very welcome
Subina Mehta
@subinamehta
@bgruening , Could you please install peptide genomic coordinate on usegalaxy.eu
Björn Grüning
@bgruening
have you added it to the shed.yml file?
if so it is already installed
Subina Mehta
@subinamehta
I did add it there
but couldnt find it on usegalaxy
ok..I see it now
thanks Bjorn
Björn Grüning
@bgruening
Sure!
Praveen Kumar
@pravs3683

Has anyone encountered Olson database or Timezone issue with R - tidyverse library in Galaxy. I am seeing this error:

Error: Unknown TZ UTC
In addition: Warning message:
In OlsonNames() : no Olson database found
Execution halted

I also used "tzdata" in XML wrapper requirements, but it still didn't help. Please suggest. Thanks!

Björn Grüning
@bgruening
yes, which R package are you using
@bernt-matthias I think you have seen this, left?
Praveen Kumar
@pravs3683
@bgruening @bernt-matthias we are using r-tidyverse version 1.2.1
M Bernt
@bernt-matthias
Sounds a bit familiar, but I can't remember. This jupyter/docker-stacks#502 suggest that adding (r-)tzdata as requirement may help
Praveen Kumar
@pravs3683
@bernt-matthias Thank you! We did try adding tzdata as requirements but it didn't help. Instead, we modified our code and replaced "readr::read_delim" with "read.delim".
David Christiany
@davidchristiany

Hi everyone, I installed msconvert from the toolshed, I use the following job_conf.xml file in order to run it with singularity (using the docker image defined in the tool requirements):

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is
     configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <destinations default='singularity_local'>
        <destination id="local" runner="local"/>
        <destination id="singularity_local" runner="local">
            <param id="singularity_enabled">true</param>
        </destination>
        <destination id="docker_local" runner="local">
          <param id="docker_enabled">true</param>
        </destination>
    </destinations>
</job_conf>

I got the following error :
FATAL: while parsing bind path: wrong bind syntax: <path>/galaxy:<path>/galaxy:rw

Did I miss something ? Or it is an error from galaxy ?
Björn Grüning
@bgruening
@davidchristiany please look at your logs and the command that is generated.
you can adjust the bind path as part of your job_conf
Martin Cech
@martenson
is there a link for today's Galaxy MS call?
Björn Grüning
@bgruening

Beschreibung:

Join Zoom Meeting
ID: 98449669068
Password: XE6UD7

Sorry, I can not attend
Martin Cech
@martenson
thanks, works
Pratik Jagtap
@pratikomics_twitter

Summary of Galaxy Mass Spectrometry October 15th meeting.

1) Metabolomics researchers - please respond to Doodle survey for a bi-monthly meeting: https://doodle.com/poll/rbemey7afzznf37g#calendar

2) Vijay Nagampalli (Blankenberg Lab) presented on Mass Spectrometry research tools needs.

3) Next Galaxy meetings –
a) Proteomics 26th November 2020 and January 7th 2021 at 1 PM GMT
b) Mass Spectrometry February 18th, 2021 at 1 PM GMT.

4) Details of prior meetings at: http://z.umn.edu/celestialmasses

5) Gitter channels:
For Proteomics: https://gitter.im/GalaxyProteomics/Lobby
For Metabolomics: https://gitter.im/usegalaxy-eu/metabolomics
https://gitter.im/workflow4metabolomics/Lobby

Björn Grüning
@bgruening
Thanks @pratikomics_twitter
M Bernt
@bernt-matthias
Hi there. I would like to get msconvert running on out instance. I have seen that it has a docker dependency. Unfortunately docker is not an option on our cluster, but singularity is. Would this work?
Björn Grüning
@bgruening
@bernt-matthias we never tried the Singularity option, but in theory it should work
M Bernt
@bernt-matthias
So I would need to adapt the tool xml changing docker to singularity
Björn Grüning
@bgruening
I'm not sure this will work.
Try to change your job_conf.xml file to request singularity instead of docker
the problem is that this is a docker-annotatated XML file.
not sure if aynone tried to run those tools in Singularity ever
but best is to test the singularity container outside of Galaxy at first
before you dig into the other problem
M Bernt
@bernt-matthias
Will do
M Bernt
@bernt-matthias
Can someone hae a look at galaxyproteomics/tools-galaxyp#516 Otherwise workflows do not run anymore?
Björn Grüning
@bgruening
Will do!
Thanks @bernt-matthias!
@bernt-matthias two small comments
M Bernt
@bernt-matthias
I see no comments
M Bernt
@bernt-matthias
@bgruening cant see comments
Björn Grüning
@bgruening
forget to clicke sent
M Bernt
@bernt-matthias
Can someone create secrets.PAT for the slash command workflow on galaxy proteomics