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  • Aug 19 15:38

    osallou on master

    Add debian package bx-tools/0.8… (compare)

  • Aug 19 15:38

    osallou on master

    Add debian package bx-tools/0.8… (compare)

NicoMaillet
@NicoMaillet
Ok, the Dockerfile by itself is not enought?
Björn Grüning
@bgruening
You can provide a Dockerfile to https://github.com/BioContainers/containers
But the recommend way is to go over conda these days.
Smaller containers, different container-types, proper tests ...
NicoMaillet
@NicoMaillet
Ok, thanks
Pablo Moreno
@pcm32
Hi! We are trying https://biocontainers.pro/#/multipackage for a multi container package with deeptools, but the multipackage creator only displays a single version of deeptools (3.1.3), when many more are available on bioconda.
Björn Grüning
@bgruening
@ypriverol ping!
See Pablos question.
is anyone there? One channel is probably enough?
Olivier Sallou
@osallou
it points to an other channel?? indeed, pointing to this one would be better
it seems all packages appear with a single version (just possible different sources)
Olivier Sallou
@osallou
getting multi package can be done via PR directly on https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv with your expected tools/versions in the meanwhile, but web site needs to be fixed to propose multiple versions or allow user to modify them
Olivier Sallou
@osallou
I'm trying to have a look at web site code....
Yasset Perez-Riverol
@ypriverol
I can take a look to the code
I know what is happening, I think
Olivier Sallou
@osallou
in code, you keep only "latest" version (which may not be really the latest in fact as you compare strings)
Olivier Sallou
@osallou
in "processData" you only need to comment code for package uniqueness and always push packageObject
Olivier Sallou
@osallou
@ypriverol when do you plan to fix the multi package issue?
Yasset Perez-Riverol
@ypriverol
Can you do a PR, I have other things this week here
if not, it will be by the end of the week
seretol
@seretol
Hi Guys, I have a question regarding singularity images.
There is this registry with a lot of images: https://depot.galaxyproject.org/singularity/.
However, it seems to not have as many containers as what is available for docker.
How do I go about adding missing images there (that I can find docker images for)?
Olivier Sallou
@osallou
I do not know, but biocontainers generates singularity images too now https://containers.biocontainers.pro/s3/singularity/, for bioconda i do not know where they are located.
And singularity suppots docker images
seretol
@seretol
Hi Olivier, tks for your reply. pulling the docker image is the other option I am thinking of.. I was just wondering what the bigger picture was when it comes to singularity, and also whether there was specific reasons not to push to shub.
Olivier Sallou
@osallou
the reason is you can't push to shub. You need to put your singularity recipes on shub, and they are built on hub. As we have no singularity recipe but only conda/docker ones......
seretol
@seretol
I see, tks Olivier
DavyCats
@DavyCats
Hi, would it be possible to make the biocontainer for https://anaconda.org/bioconda/chunked-scatter publicly available? I'm assuming it was generated, but is still set on private? @bgruening
Björn Grüning
@bgruening
@DavyCats done
sorry, was busy the last 10 days
DavyCats
@DavyCats
Thanks!
Olivier Sallou
@osallou
@folago basic security scan on containers is implemented. At this time, only new/updated containers are scanned. Very soon, results will be available on web site, in container details
Giacomo Tartari
@folago
Nice!!!
Michael R. Crusoe
@mr-c
@osallou yay!
Yasuhiro Tanizawa
@nigyta
I have added the recipe to bioconda (https://bioconda.github.io/recipes/dfast/README.html), but it seems that the container is not available yet. The software downloads reference databases automatically after the build is completed, so the file size becomes large. Is that going to be a problem?
Björn Grüning
@bgruening
@nigyta please check again
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