galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

Björn Grüning

@bgruening

@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

Oh! I found the tools at usegalaxy.eu. Not sure how I missed those in the MTS! I'll point the user to the other server. Tx!

Alexander Lenail

@zfrenchee

Is it possible in 18.01 to run tools on subsets of collections, or to "explode"/"eject" collections into individual history items?

Alexander Lenail

@zfrenchee

@jmchilton

John Chilton

@jmchilton

You can drag and drop individual items into the tool form - if you have a more systematic way to indentify the elements there is also a tool that filters a collection from a tabular file - this isn’t super straight forward but it enables a high level of tracking and use within workflows

There isn’t an explode tool though in 18.05

I meant 18.01

Alexander Lenail

@zfrenchee

Thanks!

Jennifer Hillman-Jackson

@jennaj

Does anyone know if Deseq2 in Galaxy can be configured to run with single-end data? Or is paired-end input required?

Björn Grüning

@bgruening

paired end is not required

DeSeq2 is only taking counts and don't care about single/paired

Jennifer Hillman-Jackson

@jennaj

Ok, there must be something else wrong with the inputs. Another bug report had the same error message and paired end inputs were used. There was only one replicate per condition in that example - maybe the counts are too sparse to do the DE.

Dave B.

@davebx

whomever implemented the sort flag for tool test outputs, I owe you a beer

Alexander Lenail

@zfrenchee

Hi folks,
I'm impersonating one of my users, doing some analysis. I run a tool on a collection, which works. I try to run the next tool, and get

Error executing tool: User does not have permission to use a dataset (49914) provided for input.

Does anyone know what might cause this?

Alexander Lenail

@zfrenchee

how is it possible that someone doesn't have permission on a dataset they generated in their history?

Could it be because the datasets are a subset of a collection? (Selected via drag-drop)

Alexander Lenail

@zfrenchee

Strangely, i can run a tool against the whole collection, but not 4 of the datasets inside via the drag-drop/

@jmchilton does this sound right to you?

John Chilton

@jmchilton

Ewww - that is not good. I can try checking it out tomorrow and see what the problem might be.

Any clue how the user generated that collection? Was imported, created by a tool, etc...?

Alexander Lenail

@zfrenchee

@jmchilton created by a tool. I'm running my own galaxy btw, off @bgruening 's 18.01 image. The tool I used was samtools sort, and the one that doesn't work is picard's Merge Sam on a subset of the BAM files in the collection of sorted BAMs output by samtools sort
.

Alex Buchanan

@buchanae

Hello. We're struggling to understand how best to manage a growing community of galaxy wrappers in github. Can someone help me understand how galaxy/iuc is managing it's tools in github when the toolshed is based on mercurial? Is there an automated sync process that takes the github repo and updates a toolshed server?

We're coming up with ad hoc ways to manage tools and versions, but I'd love to follow the best practices. Unfortunately, mercurial is not used here, and github is the standard.

Martin Cech

@martenson

@buchanae IUC uses Travis and Planemo to automatically lint, test, and upload all tools in the repository.

http://planemo.readthedocs.io/en/latest/

https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml

https://travis-ci.org/galaxyproject/tools-iuc

these links should get you started

the fact toolshed is using mercurial should be completely transparent to the user, it offers API for uploading (that Planemo uses)

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