Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • 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
    cpreviti synchronize #2267
  • 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
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/
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.
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?
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