Singularity container for deepTools?

Question

[Ann Loraine]

Hi!

I'm looking for a Singularity (first choice) or Docker (second choice) container with deepTools installed.

Does anybody know of a repository that contains this?

(I'm running it in a cluster environment with Singularity but not Docker daemon installed, but in theory I can run a Docker container under Singularity, so either would be fine, I guess!)

-Ann

Answer 1

[ATpoint]

I see three options:

1) Obtain a Singularity container directly via Galaxy:

wget --no-check-certificate https://depot.galaxyproject.org/singularity/deeptools%3A3.5.1--py_0

2) Convert a Docker container from Quay to create a Singularity image:

singularity pull docker://quay.io/biocontainers/deeptools:3.5.1--py_0

From what I know, if a software exists at conda then it also exists as container in Quay and Galaxy.

3) In case none of that is an option (e.g. you do not find suitable container from above sources) then create your own Docker container, install whatever you need via conda into it, and then convert to Singularity, as described Building Docker images

[Ann Loraine]

I think it worked.

I used:

singularity pull docker://quay.io/biocontainers/deeptools:3.5.1--py_0

which downloaded the Docker image and converted it to a '"sif" (singularity) image file.

Then I tried:

[aloraine@str-i1 nextflow_deepTools]$ singularity run deeptools_3.5.1--py_0.sif bamCoverage --version
INFO:    Converting SIF file to temporary sandbox...
WARNING: Skipping mount /usr/local/singularity/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
bamCoverage 3.5.1
INFO:    Cleaning up image...

which seems to have executed without an error - just a warning.

[Devon Ryan]

The good news is that docker containers are made for all bioconda packages automatically (they're used in the testing step, so they're made anyway). The Galaxy folks then convert I think all of them to singularity every day or two (Björn always mentions there's a huge backlog when I perform the twice-yearly bioconductor upate, which gives credence to this).