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 ...
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.)
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?
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?
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 :)
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/