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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
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
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    bernt-matthias edited #2269
  • Jan 31 2019 12:40
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  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
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    cpreviti synchronize #2267
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    cpreviti synchronize #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
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    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
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
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.
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/