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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
    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
Björn Grüning
@bgruening
@moskalenko its called conda-recipe and you can find them here: https://github.com/bioconda/bioconda-recipes/
Oleksandr Moskalenko
@moskalenko
@bgruening I mis-used the 'recipe' word I guess. I am looking for the backend code that the builder is using to create a container.
i.e. container recipe for docker build or singularity build
that is created from the bioconda recipe at run time.
Björn Grüning
@bgruening
So there is no such recipe. We don't use any Dockerfile or whatsoever. We straight copy conda into a Docker container
all the magic is in galaxy-lib
Brad Langhorst
@bwlang
I could use a review/merge of galaxyproject/tools-iuc#2003 if anyone has a few minutes… also galaxyproject/tools-iuc#1982 is ready to merge I think.
Anthony Bretaudeau
@abretaud
I have a few minutes :)
Brad Langhorst
@bwlang
thank @abretaud - many eyes make better work - tests for cov bed running now ;)
Anthony Bretaudeau
@abretaud
cool!
Nicola Soranzo
@nsoranzo
galaxyproject/tools-iuc#2001 is also ready, if anyone has free time
Anthony Bretaudeau
@abretaud
done :)
Nicola Soranzo
@nsoranzo
Thanks @abretaud! Trying to clean up the backlog before the holidays!
Alexander Lenail
@zfrenchee
Does anyone have experience with nested workflows which operate on collections?
I'm having an issue: I'm trying to make a workflow which contains two subworkflows, each of which take a collection and return a collection
I can't drag a noodle from the output of the first to the input of the second
Dannon
@dannon
Just created two new categories in the toolshed "GIS - Tools related to Geographic Information Systems" and "Ecology - Tools related to ecological studies".
If anyone has feedback on the names/descriptions, now would be the time -- these specific categories were requested by Yvan for Galaxy-E related work.
Alexander Lenail
@zfrenchee
@mvdbeek @bgruening do you know about nested workflows? Who is good to ask?
Dannon
@dannon
@zfrenchee The galaxyproject/Lobby channel might be better for this one? John might be a good resource, though.
Björn Grüning
@bgruening
@zfrenchee something like that? galaxyproject/galaxy#6518
Dave B.
@davebx
does the tool command block have a meta-variable for job working directory?
Nicola Soranzo
@nsoranzo
\$PWD ?
Jennifer Hillman-Jackson
@jennaj
usegalaxy.eu question -- if I didn't get this right could someone from the .eu team take a look at their data? I don't recognize the exact error and am not 100% sure it isn't a server side issue. Trinity is problematic at .org right now, not sure abt status of Trinity/Rsem at .eu
Dave B.
@davebx
correction, new error follows: is there one I can also use in a <configfile> block?
Alexander Lenail
@zfrenchee
@bgruening not quite like that -- I can't even wire the workflow steps together with noodles.
Alexander Lenail
@zfrenchee
Should I open an issue about this against galaxy? Has anyone else every successfully run a nested workflow where the inner workflow takes and returns a collection?
Robert Leach
@hepcat72
Is anyone working on an svtyper wrapper or does anyone have one that isn't on the toolshed?
Björn Grüning
@bgruening
I'm not aware of anyone, but it also on my long todo list :)
Robert Leach
@hepcat72
@bgruening - I may give it a go if I don't get too bogged down on another project today. I'm a novice though. I've only been through the process 1 and a half times thus far using the simplest of mechanisms. Perhaps it could serve as a starting point for someone more adept at it.
Björn Grüning
@bgruening
We can help you and review your work if you like.
Bérénice Batut
@bebatut
Hi @/all. The GTN CoFest will on Friday: galaxyproject/training-material#939
We also plan to have the same day a GTN meeting: galaxyproject/training-material#954
Robert Leach
@hepcat72
@bgruening Absolutely!
Robert Leach
@hepcat72
If a tool requires an index file for a bam or a fasta file, is that typically handled in the command tag or is there some other built-in mechanism?
Robert Leach
@hepcat72
So, I have 2 optional output files, but I can't figure out how to get the tests to pass. They keep complaining about bad file descriptors. I assume it's the optional files that were not created. How do I configure the tests to not look for these files?
Björn Grüning
@bgruening
If a tool requires an index file for a bam or a fasta file, is that typically handled in the command tag or is there some other built-in mechanism?
In the command section
can you share the tests here so we can have a look?
Robert Leach
@hepcat72
I'm past that error. Asked Lance about it at lunch and he was able to help.
Scott Ouellette
@scottx611x

Hi folks I've been having troubles running Salmon consistently on my Cloudman cluster. Have been running into seg faults when specifying > 1 ~4Gb fastqs as input (from a list collection as well as n input datasets). Ive been seeing this on m4.2xlarge and m4.4xlarge worker nodes. I think I've exhausted all different SLURM configurations in my job_conf.xml to try and combat this

Has anyone run into something similar, and if not where would be the best place to file an issue? Thanks!

Carrie
@cganote
Can you try running it through gdb? Sometimes that'll give you a line it dies on]
Robert Leach
@hepcat72
@bgruening - I have a working / preliminary version of an svtyper wrapper on the tool shed now. I need to look into IUC requirements, so I'll probably need some edits. I'll work on that tomorrow. Heading out.
Björn Grüning
@bgruening
@hepcat72 sounds great! Let me know if you need anything!
Scott Ouellette
@scottx611x

@cganote Thanks for the suggestion! I took a couple of hours today to look into running w/ gdb, but from what I understood I would have had to recompile salmon with a debug flag (-g) beforehand, and I quickly got lost in how I would do that and be able to run it this way through Galaxy & SLURM.

What I think could be helpful is if anyone could point me to a job_conf.xml destination that has been successful in running Salmon with the galaxy.jobs.runners.slurm:SlurmJobRunner

Also if this is not the proper place to be asking such a question could someone point me in the right direction? Thanks!

Björn Grüning
@bgruening
Welcome everyone to the CoFest!
@scottx611x have you tried to run salmon locally without Galaxy and Slurm?
Is this Salmon version from the TS and uses the Conda dependencies?