Add vcftools and htslib

[mribeirodantas]

No description provided.

[bgruening]

thanks @mribeirodantas

[mribeirodantas]

Thanks, @bgruening ! I was able to find the container image by pulling the image last added to quay.io/biocontainers, but I can't find it at https://biocontainers.pro/multipackage or with mulled-search from the galaxy-tool-util package.

Is it because it takes a while to update the search database? Is there any other way that could help me (and others) find this image?

UPDATE: I was able to find it on the biocontainers registry, but it doesn't have the tags, which makes it difficult to find it unless you already know the container name (https://biocontainers.pro/tools/mulled-v2-b9358559e3ae3b9d7d8dbf1f401ae1fcaf757de3). How can I add the tags?

[bgruening]

I'm not responsible for the registry and in fact, do not use it. I go directly to quay.io.
Tags are imho only possible to add via the Dockerfile builds, those ones here are automatic.

What have you tried with mulled-search that should be able to list your image? See https://github.com/BioContainers/multi-package-containers#searching-for-containers

[mribeirodantas]

I expected mulled-search --destination quay -s vcftools tabix to return my container image. Or looking for them by vcftools and/or tabix in here: https://biocontainers.pro/multipackage

Who is responsible for that? Who can help me understand how can I make this happen? 😄

[tamuanand]

Hi @mribeirodantas

Were you looking for something like this below?

• I use this snippet (as shown below) - https://gist.github.com/peterk87/c28167ceffbb36dcbcf5b5b225c4043d

python3 multi_container_mulled_hash.py "vcftools=0.1.14-0,htslib=1.3.1-0"
Packages                   : vcftools=0.1.14-0,htslib=1.3.1-0
# packages                 : 2
Mulled name                : mulled-v2-b9358559e3ae3b9d7d8dbf1f401ae1fcaf757de3:ac05763cf181a5070c2fdb9bb5461f8d08f7b93b
Image Name                 : mulled-v2-b9358559e3ae3b9d7d8dbf1f401ae1fcaf757de3
Version/Tag Name           : ac05763cf181a5070c2fdb9bb5461f8d08f7b93b
Quay.io URL                : https://quay.io/repository/biocontainers/mulled-v2-b9358559e3ae3b9d7d8dbf1f401ae1fcaf757de3
Docker pull command (quess): quay.io/biocontainers/mulled-v2-b9358559e3ae3b9d7d8dbf1f401ae1fcaf757de3:ac05763cf181a5070c2fdb9bb5461f8d08f7b93b-0

[mribeirodantas]

Thanks, @tamuanand ! 😉

[bgruening]

Its documented here: https://github.com/BioContainers/multi-package-containers#searching-for-containers

Can you provide me your bash command for mulled-search and the results? If its not working we should fix it :)

[mribeirodantas]

The following command returns no results: mulled-search --destination quay -s vcftools. mulled-search --destination quay -s vcftools,htslib neither.