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  • Jun 02 16:42
    lucacozzuto commented #374
  • Jun 02 16:37
    bgruening commented #374
  • Jun 02 16:09
    lucacozzuto commented #374
  • Jun 02 15:44
    bgruening commented #374
  • Jun 02 15:34
    osallou commented #374
  • Jun 02 15:32
    lucacozzuto opened #374
  • May 29 16:38
    biocontainers-bot commented on 6935046
  • May 29 16:25

    osallou on master

    fix biotools and name (compare)

  • May 29 14:22
    biocontainers-bot commented #373
  • May 29 14:22
    biocontainers-bot commented on 9972d8f
  • May 29 14:20
    biocontainers-bot commented #373
  • May 29 14:20

    osallou on master

    add bwa 0.7.17 (#373) * add bw… (compare)

  • May 29 14:20
    osallou closed #373
  • May 29 14:19
    biocontainers-bot commented #373
  • May 29 14:18
    biocontainers-bot commented #373
  • May 29 14:18
    ychenbioinfo synchronize #373
  • May 29 14:14
    biocontainers-bot commented #371
  • May 29 14:14
    biocontainers-bot commented on b4f96da
  • May 29 14:12
    biocontainers-bot commented #371
  • May 29 14:12
    biocontainers-bot commented #371
Stian Lågstad
@stianlagstad
I found a bunch more dead links in the repository. If anyone could help sort those out that would be great :) https://github.com/BioContainers/specs/issues/98#issuecomment-596413822
Yasset Perez-Riverol
@ypriverol
Thanks a lot, I will try to fix them
Stian Lågstad
@stianlagstad
Thanks! :)
Jonathan Manning
@pinin4fjords
Morning all- could someone take a look at this tiny PR? BioContainers/multi-package-containers#1200 ?
Björn Grüning
@bgruening
done
Jonathan Manning
@pinin4fjords
Awesome - thanks @bgruening .
Jonathan Manning
@pinin4fjords
Morning all- could the container for scxa-plots be made public please? bioconda/bioconda-recipes#20912 . Or is there a way of me doing this?
Björn Grüning
@bgruening
have you merged without the bot?
Jonathan Manning
@pinin4fjords
Yes, I did it before I could stop my fingers, sorry. Are containers made public if I did it with the bot as I should?
Björn Grüning
@bgruening
lol
public
Jonathan Manning
@pinin4fjords
Thanks! So normally the bot would have done it?
Björn Grüning
@bgruening
yes
Jonathan Manning
@pinin4fjords
Awesome- thanks Bjorn. Hope you guys are all coping with the Covid.
Björn Grüning
@bgruening
We do our best!
\all what about a hackathon, now that most of you are at home!
Doing something good?
Who would be in?
Jonathan Manning
@pinin4fjords
Could be fun! Will check with the Overlord.
Björn Grüning
@bgruening
lol
greeting to the Overlord!
Eric T. Dawson
@edawson
Hi all! Looks like the link to the Biocontainers base image in the docs is dead: https://biocontainers-edu.biocontainers.pro/en/latest/best_practices.html#image-name-and-versions
And biocontainers-edu has invalid httpscertificate...
Michael R. Crusoe
@mr-c
Where do I send a PR to make a biocontainer from Debian's package of vg?
Yasset Perez-Riverol
@ypriverol
The search and web is back
Trying to recover our CI
Björn Grüning
@bgruening
@mr-c in the meantime you could create a conda package
Michael R. Crusoe
@mr-c
@bgruening True! The Debian package was a ton of work, so I went ahead and https://hub.docker.com/repository/docker/biocrusoe/vg & BioContainers/containers#361
For whoever makes the conda package, special care will need to be taken so that it runs on different X86 processors that might not have the same SIMD support.
Björn Grüning
@bgruening
So no Conda package from you then I guess :)
I'll see if I can get more of the patches upstreamed
Yang Xu
@JasonYangShadow
https://bioconda-recipes-demo.readthedocs.io/en/latest/guidelines.html Is this link correct for doc of bioconda recipes?
Karl Nordström
@karl616
Hi, quick question: is there a way to have tzdata included in a biocontainer?
Björn Grüning
@bgruening
@karl616 in all?
Karl Nordström
@karl616
@bgruening no, one particular. It is a dependency of r-readr, but not specified as such
Björn Grüning
@bgruening
the r-readr container?
this will add a new container
Karl Nordström
@karl616
I don't think that container will work. I found it with the containers I created last week: BioContainers/multi-package-containers#1263 The r-readr package needs TZ data: tidyverse/readr#952 but it isn't available in the container
I understand why it isn't. I'm not sure which package holds TZ data, tzdata maybe, but it is not specified as dependency of the package: https://cran.r-project.org/web/packages/readr/index.html
Björn Grüning
@bgruening
@karl616 ah, I see
but then please add this dependency to https://github.com/conda-forge/r-readr-feedstock
and it will work
Karl Nordström
@karl616
I can do that, would you know which package to add? If not, I try to figure it out
Björn Grüning
@bgruening
No really the python package does not depend on anything special: https://github.com/conda-forge/pytzdata-feedstock/blob/master/recipe/meta.yaml
Karl Nordström
@karl616
I found the tzcode package as well. Installing it and r-readr and to my understanding, the latter still picks up the system tzdata folder... I'll try to add it to my container as a test
Karl Nordström
@karl616
Alternatively, I'll try to map the folder into the container, but defeats the purpose of a container to a certain degree