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galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

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Repo info

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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
Jan 31 2019 14:15

cpreviti synchronize #2267
Jan 31 2019 12:42

bernt-matthias review_requested #2269
Jan 31 2019 12:42

bernt-matthias edited #2269
Jan 31 2019 12:41

bernt-matthias edited #2269
Jan 31 2019 12:40

bernt-matthias synchronize #2269
Jan 31 2019 12:13

cpreviti commented #2267
Jan 31 2019 12:07

nsoranzo commented #2267
Jan 31 2019 12:01

cpreviti synchronize #2267
Jan 31 2019 11:21

cpreviti synchronize #2267
Jan 31 2019 09:47

cpreviti synchronize #2267
Jan 31 2019 09:27

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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

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/

The tool is not installed at either usegalaxy.* .. so this error is on a local, docker, etc with the tool installed from the existing MTS repo

Jennifer Hillman-Jackson

@jennaj

Is this a bug with Salmon output files? Or should the output format be configurable?
Seems like a normal use case, but I haven't used the tool that much. https://biostar.usegalaxy.org/p/23985/#27525

Oleksandr Moskalenko

@moskalenko

I'm doing a lot of tool installs to switch to conda for 18.01 from my much older previous production instance and I'm noticing a few broken packages in the toolshed. Where should I report the bugs?

Nicola Soranzo

@nsoranzo

Depends on who's the tool author/owner

Oleksandr Moskalenko

@moskalenko

What about devteam and iuc

Björn Grüning

@bgruening

https://github.com/galaxyproject/tools-iuc/issues

Oleksandr Moskalenko

@moskalenko

Got it, thanks Bjorn.

Jennifer Hillman-Jackson

@jennaj

@yhoogstrate Do you know if there are plans to update Varscan to include the newer "somatic" function? If not, what would be your (and others) suggested tool alternative?

question was asked here: https://biostar.usegalaxy.org/p/27507/

function: http://varscan.sourceforge.net/somatic-calling.html

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