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
Nicola Soranzo
@nsoranzo
I think so too
Dave B.
@davebx
ok, I'll change the vcflib versions to +galaxy1
Nicola Soranzo
@nsoranzo
@mvdbeek If you're OK with the changes I've made to galaxyproject/tools-iuc#1791, I think we can merge it.
Marius van den Beek
@mvdbeek
yeah, sure! thanks @nsoranzo
Nicola Soranzo
@nsoranzo
+galaxy0 should also be fine, right?
So we use the same convention as the Conda build number of starting at 0
Marius van den Beek
@mvdbeek
Sure, I was considering that we already had a .0 suffix
but any way is fine with me
Anton Nekrutenko
@nekrut
@mvdbeek @nsoranzo if you get a chance please take a look at galaxyproject/tools-iuc#1787 I’m trying to finish a paper that depends on snpEff
Marius van den Beek
@mvdbeek
@nekrut reviewing now
Anton Nekrutenko
@nekrut
merci
Lance Parsons
@lparsons
I've gotten a request from a user to install Kraken on our local Galaxy. I've not used this tool before, and I'm concerned about the warnings in the readme about the database needing to be local, etc. Does anyone have experience getting this tool working, esp. in Galaxy? Any tips?
Martin Cech
@martenson
We have Kraken on Main, @davebx did you install it?
Dave B.
@davebx
I'm pretty sure that was me
Lance Parsons
@lparsons
@davebx Did you have to do anything special with the database? And was it a lot of work? I'm reluctant to install and maintain it if it's going to be difficult unless I know there are strong interest here. But if it's not too bad, I'm happy to provide it.
Dave B.
@davebx
there should be a data manager that takes care of the database situation
Lance Parsons
@lparsons
Oh really? I just assumed given all the warnings about no NFS, etc. that I'd have to handle that administratively...
Excellent, looks like there is a data manager. I'll look into it, thanks @davebx !
Lance Parsons
@lparsons
Now, on a somewhat related note, I'd like to build a STAR index for GRCh38 (Ensembl), but it seems that the data manager for STAR has no way to specify limitGenomeGenerateRAM and the default setting seems far to low (it claims to want 128GB while default is 28GB). Any tips on doing this behind the scenes? Should I just do it on the command line myself and hand edit the .loc file? Thanks again all.
Anton Nekrutenko
@nekrut
looks like @natefoo type of question
Nate Coraor
@natefoo
the DM should probably be updated to support $GALAXY_MEMORY_MB
Lance Parsons
@lparsons
@natefoo Yeah, that makes sense. I figured there was some parameter for Galaxy memory. In the meantime, I guess I'll just see about building it offline and editing the .loc file.
Nate Coraor
@natefoo
it's new and only implemented for slurm though.
but yeah that sounds like the solution for now unfortunately. =(
Jennifer Hillman-Jackson
@jennaj
Reported problem with nginx in a docker Galaxy. Could someone help or is this a known? The workaround for the getgalaxy.org version was already posted but I never tested that directly: https://biostar.usegalaxy.org/p/26728
Lance Parsons
@lparsons
So, data managers don't actually update the tool_data_table_conf.xml or the rnastar_index2.loc files? Is there some data manager only copy that gets merged? Just trying to sort out what file(s) I need to update to add a new index manually these days.
And perhaps this is better asked in galaxyproject...
Jennifer Hillman-Jackson
@jennaj
Docker/download/nginx issue discussion is moved to the docker channel https://gitter.im/bgruening/docker-galaxy-stable?at=5ab9436f5f188ccc15fbdd8f
Marius van den Beek
@mvdbeek
@lparsons any loc file of your liking, they all get merged.
if you have one in the root of your tool-data dir that would probably be the most appropriate for manual builds
Lance Parsons
@lparsons
Thanks @mvdbeek . Do I need to update tool_data_table_conf.xml?
Or should I just leave that alone?
Nicola Soranzo
@nsoranzo
Leave it
Lance Parsons
@lparsons
Thx!
Wolfgang Maier
@wm75
The latest planemo docs mention GALAXY_MEMORY_MB and GALAXY_MEMORY_MB_PER_SLOT, but the samtools sort wrapper linked as a usage example does not seem to use either of them yet. So how are tools supposed to work with these settings? Specifically, how should you decide which one to look for?
Marius van den Beek
@mvdbeek
GALAXY_MEMORY_MB_PER_SLOT is useful if the memory scales with the CPU, GALAXY_MEMORY_MB is the total memory available for the job
samtools for example scales the required memory per thread, so there GALAXY_MEMORY_MB_PER_SLOT is appropriate
Wolfgang Maier
@wm75
hmm, I guess my question was from a tool wrapper's author perspective. How should the wrapper know which of the two variables to expect. In the PR you linked to the samtools wrappers simply use GALAXY_MEMORY_MB so that's not explaining that.
or do admins have to check each wrapper to figure out which of the two variables to use?
Marius van den Beek
@mvdbeek
They're all there
and if not it uses the fallback value, just like for GALXY_SLOTS
Well, they're not always there, certainly not by default in older galaxy instances, but you can either specify a fallback like in the samtools PR or check if the variable is defined
Wolfgang Maier
@wm75
I'm sorry if I'm asking a dumb question repeatedly, but I'm still not getting it: in https://github.com/galaxyproject/tools-iuc/pull/1748/files all tool wrappers except the one for hisat2 use GALAXY_MEMORY_MB. Now if an admin configures job runners to set GALAXY_MEMORY_MB_PER_SLOT that gets ignored or not? Conversely, the hisat2 wrapper would ignore GALAXY_MEMORY_MB then?
Marius van den Beek
@mvdbeek
it's not dumb questions, I guess we're not explaining this in all details, ${GALAXY_MEMORY_MB:-768} is syntax for if GALAXY_MEMORY_MB is set, use that value, else 768 using bash parameter substitution syntax. An admin shouldn't need to set anything for GALAXY_MEMORY_MB_PER_SLOT, that can be calculated from GALAXY_MEMORY_MB
Wolfgang Maier
@wm75
agreed.
Marius van den Beek
@mvdbeek
from the admin perspective the documentation is here: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/cluster.md