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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
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  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
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  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
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  • 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
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    nsoranzo commented #2267
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Maybe the install
Brad Langhorst
@bwlang
strange… metaphlan2 pkg exists in pkgs, but is not in the environment. I’m going to add it manually - maybe there is some dependency issue - though nothing complained until i tried to run the tool.
aha!
Installing conda-forge::click-6.7-py_1 requires a minimum conda version of 4.3.
that should probably cause some kind of error during installation of the tool… galaxy bug i guess.
just have to manually update conda...
Björn Grüning
@bgruening
The biocontainers do come with bash by default. Its a busybox+static bash
Björn Grüning
@bgruening
The biocontainers do come with bash by default. Its a busybox+static bash
Alexander Lenail
@zfrenchee
Is there a guide for building galaxy tools from docker containers somewhere (instead of python / conda packages)?
Alexander Lenail
@zfrenchee
Where the execution of the tool is a docker run ...
Martin Cech
@martenson
@zfrenchee you probably can to start here: https://docs.galaxyproject.org/en/master/admin/special_topics/mulled_containers.html
Lance Parsons
@lparsons
Sorry for the cross-post, but wasn't sure which channel was best: Does anyone have any advice on tools/methods to plot genome coverage across one sequence id from a BAM file using a "custom" reference in Galaxy? I wasn't able to get Trackster to work at all (problems with datasets in collections, custom reference, etc.)
Brad Langhorst
@bwlang
i just use igv. you might want to have a look at mosdepth https://github.com/brentp/mosdepth
^^@lparsons
Lance Parsons
@lparsons
Thanks @bwlang , I'll check it out. Is there a Galaxy wrapper by chance?
Brad Langhorst
@bwlang
not sure… have not seen one.
Lance Parsons
@lparsons
ok, thanks.
Anton Nekrutenko
@nekrut
@lparsons DeepTools?
Devon Ryan
@dpryan79
@lparsons You might be able to use either hicPlotTads (from HiCExplorer) or pyGenomeTracks. They're essentially the same tool, but I know the former is definitely available in the toolshed.
Björn Grüning
@bgruening
pyGenomeTracks needs a proper Galaxy integation. We will work on this as soon as we are back. hiCPLotTads has the TAD plot currently mandatory, that needs to be changed.
I think we are going to deprecated the hicPLotTads in favor of pyGenomeTracks
Gildas Le Corguillé
@lecorguille
Hum … I though that there was a tool within planemo to test a whole workflow but I can’t find where. Did I dream?
Björn Grüning
@bgruening
@lecorguille planemo-dev should have this
Jennifer Hillman-Jackson
@jennaj
@lparsons Hi - there is a question about the install of Cutadapt in a local. Could you help them? https://biostar.usegalaxy.org/p/27434/
Jennifer Hillman-Jackson
@jennaj
@jj-umn @bwlang GMAP/MiGMAP question https://biostar.usegalaxy.org/p/27374/
I am not sure which tool version, Galaxy version, etc is in use and I pointed them here for help. I don't know either of these wrappers well enough to help.
Alexander Lenail
@zfrenchee
What is the system path for the local reference data config file in galaxy?
Jennifer Hillman-Jackson
@jennaj
A thank you for the featureCounts annotation update! Nice! https://biostar.usegalaxy.org/p/27461/
Björn Grüning
@bgruening
@jennaj such a big difference is scary isn't it?
Jennifer Hillman-Jackson
@jennaj
yeah, it's the gene_id/transcript_id being the same value in UCSC GTFs. I know why the TB outputs the data that way but many people completely miss it .. and then get odd results --since the counts are really by transcript, not gene :(
Björn Grüning
@bgruening
either way I added a small comment to biostar, feel free to accept the answer :)
Jennifer Hillman-Jackson
@jennaj
:)
Jennifer Hillman-Jackson
@jennaj
Hi - does anyone know if there are plans to wrap the Torrent Suite? https://github.com/iontorrent/TS
From a question at Biostars: https://biostar.usegalaxy.org/p/27473
Björn Grüning
@bgruening
Not that I'm aware of.
Jen IonTorrent was a sponsor for GCC at some point right?
Mabye they are interested in developing integrations?
If they have someone to work on it, I'm happy to help.
@jennaj https://github.com/iontorrent/TS/tree/f2205b61dcf47b69fbef27ec7185a0a4de817106/Analysis/TMAP/scripts/galaxy
look at that?
would be nice to ping them, if they are willing to update them and maybe contribute to IUC or offer conda integration
Jennifer Hillman-Jackson
@jennaj
ooh - I couldn't find that link!
Ok, I'll share that with the biostar post. I think someone from IUC should make contact, yes? And they were a sponsor, maybe this will work out :)
Björn Grüning
@bgruening
@jennaj I think you should make contact :)
You Main team member :)
Jennifer Hillman-Jackson
@jennaj
Ah, ok, will check with team first to make sure there isn't some contact going on already. Thanks!
Björn Grüning
@bgruening
Thanks Jen!
mblue9
@mblue9
Thanks to @jennaj and @bgruening for the notifications about those Biostars posts on Cutadapt featureCounts! (It made me finally get around to making a Biostars account :smile:)
Jennifer Hillman-Jackson
@jennaj
@CollardT You are working on the updated Ballgown wrapper, correct? A question came in about an error.
I haven't seen this before so don't know how to solve it or if this is a known issue -- is there anything you would like to add to my reply? https://biostar.usegalaxy.org/p/27454/