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  • 17:36
  • 13:21
    engycliu starred BioContainers/containers
  • Nov 29 08:12
    biocontainers-bot commented #350
  • Nov 29 08:09
    biocontainers-bot commented on b01e5a6
  • Nov 29 08:07
    biocontainers-bot commented #350
  • Nov 29 08:06

    osallou on master

    Philosopher added to BioContain… (compare)

  • Nov 29 08:06
    osallou closed #350
  • Nov 29 08:06
    biocontainers-bot commented #350
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    biocontainers-bot commented #350
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    ypriverol synchronize #350
  • Nov 28 21:36
    biocontainers-bot commented #350
  • Nov 28 21:32
    biocontainers-bot commented #350
  • Nov 28 21:32
    ypriverol synchronize #350
  • Nov 28 17:56
    biocontainers-bot commented #350
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    biocontainers-bot commented #350
  • Nov 28 17:52
    ypriverol synchronize #350
  • Nov 28 17:33
    biocontainers-bot commented #350
  • Nov 28 17:32
    ypriverol opened #350
  • Nov 26 20:29
    Marufsahariar starred BioContainers/containers
Björn Grüning
@bgruening
there might be a slight delay in publishing it
Yasuhiro Tanizawa
@nigyta
@bgruening Thank you! I have pulled the container and confirmed that it works as expected.
Björn Grüning
@bgruening
awesome, thanks!
Nathan Sheffield
@nsheff
What am I doing wrong? docker pull biocontainers/samtools
Using default tag: latest
Error response from daemon: manifest for biocontainers/samtools:latest not found
Michael R. Crusoe
@mr-c
@nsheff I can reproduce your error. Maybe try quay.io ??
FYI, there is no latest
So docker pull biocontainers/samtools:v1.7.0_cv4 works
Nathan Sheffield
@nsheff
Got it, thanks, that was it! it's funny that for such a simple thing dockerhub is so unintuitive... it says docker pull biocontainers/samtools right there on the main page. But I guess it assumes there's a latest tag.
Maxime HEBRARD
@mhebrard
Hello Here, I am using picard tools in conda environment. I succeed to run picard using the picard MarkDuplicates I=... syntax. I wonder how I can use the new syntax -I ... ? that require to pass the system property -Dpicard.useLegacyParser=false but I am not sure how to use that with the shell command picard from within conda ^^"
Michael R. Crusoe
@mr-c
Can someone add Debian-Med & https://people.debian.org/~tille/debian-med/logos/med-06.jpg to the "Partners" section of https://biocontainers.pro ?
Olivier Sallou
@osallou
For picard. I suppose 'picard' is only a wrapper shell that does something like java -jar xxx ...
So you just need to execute the 'real' cmd to add system props, and not use the picard shortcut
Giacomo Tartari
@folago
What is the story about GATK license? We cannot include the jar in the container?
Björn Grüning
@bgruening
Latest version of GATK is open source
Giacomo Tartari
@folago
4.x?
Björn Grüning
@bgruening
I think <4 was problematic
Giacomo Tartari
@folago
ah damn… I thik we are stuck witht 3.6.0
OK thanks!
Björn Grüning
@bgruening
mh, maybe below 3 was problematic?
eitherway, try latest builds from https://quay.io/repository/biocontainers/gatk?tab=tags
they should have the jar
Giacomo Tartari
@folago
Björn Grüning
@bgruening
ok, I see
the 4 version is BSD licensed
Giacomo Tartari
@folago
OK
Björn Grüning
@bgruening
package name gatk4
Giacomo Tartari
@folago
I am afraid we need 3.6
I’ll look for alternatives
Björn Grüning
@bgruening
sorry :(
you could ask if they changed the license retrospectively
Giacomo Tartari
@folago
No probs, license are weird that way
yeah good idea, i’ll poke around a bit
Evan Floden
@evanfloden
For multi containers, I understand there is the helper for going from toolnames -> mulled container. Is there a helper to know what containers have already been built?
Björn Grüning
@bgruening
you could use mulled-search
What WMS do is they create the name, look it up in Quay.io or Singularity and if not available, build it locally
Giacomo Tartari
@folago
how do it recover the tools and version in a mulled-v2 multi-tools container?
Giacomo Tartari
@folago
for example quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:23592e4ad15ca2acfca18facab87a1ce22c49da1-0
i know is bwa and samtools but i have no clue on the versions
Hervé Ménager
@hmenager
Looks like the biocontainers.pro registry is broken
https://biocontainers.pro/#/registry is popping up a "server error" when opening the page
Olivier Sallou
@osallou
there is indeed a 500 error. @ypriverol can you have a look at what is going wrong?
Hervé Ménager
@hmenager
:+1:
Yasset Perez-Riverol
@ypriverol
I will have a look
Hervé Ménager
@hmenager
thank you @ypriverol !
Yasset Perez-Riverol
@ypriverol
Error fixed +1