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  • Jan 31 22:04
    foellmelanie closed #336
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    foellmelanie opened #340
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    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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    Modify for new FlashLFQ release… new test data for new version (compare)

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  • Jan 23 06:38

    bgruening on unipept4.0

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  • Jan 23 01:47

    jj-umn on master

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

Krzysztof Poterlowicz
@kpoterlowicz
Hi I am wondering if you can recommend some introductory slides for GTN metaproteomics training https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html ?
Pratik Jagtap
@pratikomics_twitter
Hello @kpoterlowicz - we have some introductory slides from a 2017 workshop (http://z.umn.edu/sw1presentation). Would these work? I can modify and send them to you.
Krzysztof Poterlowicz
@kpoterlowicz
Hi @pratikomics_twitter ,thank you very much, this is what I have been looking for ! The pdf under link you provided will work for me, so no need for modification If you don't mind me to use it
Pratik Jagtap
@pratikomics_twitter
@kpoterlowicz - excellent! Let us know if you need anything more.
Björn Grüning
@bgruening
@subinamehta does workflow testing work?
let me know if you have any Q
Subina Mehta
@subinamehta
@bgruening , I tried the test sample that you showed..that works..trying to do the same with metaproteomics workflow
I will definitely come to you if I get stuck
Björn Grüning
@bgruening
nice
pvanheus
@pvanheus
hello galaxyp folks - I got some folks here with a novel plant transcriptome... they're looking around for tools to do functional annotation... is eggnog (eggnog-mapper) appropriate?
Subina Mehta
@subinamehta
Unipept?
the new version i think works well
How many samples are we talking about??
Caleb Easterly
@caleb-easterly
I don't know too much about transcriptomics, but I think eggnog-mapper might do well, provided the transcripts are fairly long (e.g. close to full protein length). There's an option to translate from genes to protein sequences ( I don't know if this does 3-frame or not).
Björn Grüning
@bgruening
Hi all.
it seems it could replace a few steps of your workflow and take PS output direclty to create a BED file
proteomics
@proteomics_twitter
Hello Bjoern, Thanks for forwarding this. Looks like an interesting tool which can potentially take the Peptideshaker peptide report (and moFF outputs) or mzidentML output to generate GTF and BED files. I sent a message to the Galaxy-P group. It will be good to see how it fits within our current workflow.
Jim Johnson
@jj-umn

Anyone know how to deal with this Travis test error?

galaxyproteomics/tools-galaxyp#369

Get an error from continuous-integration/travis-ci/pr

Fetching package metadata ...
CondaHTTPError: HTTP 504 GATEWAY_TIMEOUT for url https://conda.anaconda.org/iuc/linux-64/repodata.json
...
conda_init failed - failed to install to '/home/travis/conda/bin/conda'
The command "planemo conda_init" failed and exited with 1 during .

Björn Grüning
@bgruening
I just restarted
looks like a timeout
Jim Johnson
@jj-umn
@bgruening Thanks. Is that something I should know how to do as well?
Björn Grüning
@bgruening
Sure :)
do you see the reload button behind every job
with this you can restart travis jobs
Jim Johnson
@jj-umn
@bgruening I've seen the rerun buttons before, but I'm not seeing them now.
Björn Grüning
@bgruening
mh
try to subscribe to this repo again on the travis CI UI
Jim Johnson
@jj-umn
@bgruening That worked. T%han ks.
Björn Grüning
@bgruening
cool!
Björn Grüning
@bgruening
Hi everyone. If someone is interested in MaxQuant in Galaxy please consider to test it here and provide feedback: https://usegalaxy.eu/root?tool_id=maxquant
M Bernt
@bernt-matthias
Anyone has an idea how to fix the error popping up here: galaxyproteomics/tools-galaxyp#378 .. seems unrelated to the PR.
Björn Grüning
@bgruening
@jraysajulga I think I have a PeptideShaker job running from you since 25 days?
Is that normal, can we kill it? :)
M Bernt
@bernt-matthias
hi there. is there a tool for mapping ncbi taxids to uniprot ids. We would like to retrieve all uniprot entries from a list of taxa.
this one?
M Bernt
@bernt-matthias
this is unfortunately for unipept not uniprot
maybe this one can be enhanced?
Björn Grüning
@bgruening
can you send an error report
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