galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

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)

Alex Buchanan

@buchanae

@martenson excellent, thank you. I'll give it a shot.

John Chilton

@jmchilton

@zfrenchee the four datasets that don't work with drag and drop - can you like view the data in Galaxy, edit attributes, download, etc...?

Alexander Lenail

@zfrenchee

@jmchilton I can. I see that the user I'm impersonating has permissions over the dataset. I can look at the top of the BAMS with the eye, I can view info with the "i" and I can edit attribute with the pencil. Everything else looks right.

It also seems to be the case that he can't run the job logged in as himself (not via an admin impersonating him). It's possible the impersonation didn't work, so to speak, and despite the Permissions saying he has permissions, somehow only the admin has permissions.

I can give you access to my galaxy to take a look if that would help. Send me a PM.

Dave B.

@davebx

I just discovered a probably known issue: creating a conda environment containing (among other things) a perl library apparently does not add /path/to/env/lib/perl/n.n.n/ to @INC

never mind, it's the tool script shebanging #!/usr/bin/perl instead of #!/usr/bin/env perl

Jennifer Hillman-Jackson

@jennaj

Hi all - are there any current plans to wrap bioconductor/maftools?

asked at https://biostar.usegalaxy.org/p/27697

If I somehow missed these in the MTS, please educate me :)

Yvan Le Bras

@yvanlebras

Hi Jennifer, I remember I saw tools using maftools R library on Github... and if I don't make a mistake, there is related tools here: https://github.com/morinlab/tools-morinlab/tree/master/tools/maftools

Jennifer Hillman-Jackson

@jennaj

Thanks Yvan - I pointed the end user to this chat, so they can use that info if they want to get involved in the dev project or make a wrapper request to the IUC. Nice find!

Yvan Le Bras

@yvanlebras

you're welcome

John Chilton

@jmchilton

@zfrenchee So the user should have access to the data and does have access to the data, the form just isn't working when dragging and dropping? At least it seems like it isn't a security problem :sweat: ... umm is there any sort of log on the backend when that happens?

Oh - one thing to try is to make sure the dataset state is 'ok' and not something like "metadata_error"

Alexander Lenail

@zfrenchee

@jmchilton how do I check the dataset state?

Nicola Soranzo

@nsoranzo

I'm planning to extend the filter_by_fasta_ids tool from tools-galaxyp to be a more generic FASTA filter tool, e.g. to also be able to filter using regular expressions on the headers or the sequence, or filter by sequence length as in https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length

@bgruening : Should I modify the tools-galaxyp tool or create a new one in tools-iuc repo?

Björn Grüning

@bgruening

please modify the galaxyp one

I think we are also fine to move this into tools-iuc if you think this is needed

Nicola Soranzo

@nsoranzo

galaxyp repo works for me, thanks!

Murilo Machado

@mrlmachado

Hi all, I found myself now, after some weeks trying to solve this, without any ideas for solving what I faced in my local galaxy server. I'm runing version 18.01 of galaxy with nginx and interactive environment enabled and postgresql and I build a tool with Gviz package dependency resolving by conda. Galaxy resolve all dependencies correctly but when I call IdeogramTrack function from R it throws a Bad Request 400 Error only within galaxy environment. If I execute from the server with Rscript, my code runs perfectly. I tried disable GIE and enable debug level of logs from nginx and wsgi but no success to find what is causing this error. I know this function call ucsc uri to download hg tables, but it works from the very server where galaxy is running and within galaxy it does not work. I really need help here to understand what is happening and how can I solve this out. Sorry for the long text and sorry again if this is not the right place to ask for help...

Nicola Soranzo

@nsoranzo

@mrlmachado You may have better luck on Join the chat: https://gitter.im/galaxyproject/Lobby

Brad Langhorst

@bwlang

just got this error when i tried to use a just installed copy of trim galore

Failed to activate conda environment! Error was:
Not a conda environment: /mnt/galaxy/data/galaxy/tool-deps/_conda/envs/__trim-galore@0.4.3

Is this a tool bug or have I misconfigured my galaxy ? I recently upgraded, but conda resolution was working fine before .

Brad Langhorst

@bwlang

trimmomatic seems to have installed and worked… so maybe a tool issue?

Ghost

@ghost~5772e7e2c2f0db084a206e1b

can you activate the environment ? this is not something that tools have control over

i.e source activate __trim-galore@0.4.3 with conda at /mnt/galaxy/data/galaxy/tool-deps/_conda/bin on PATH

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