Questions tagged [docker]

Docker is a computer program that performs operating-system-level virtualization, also known as "containerization".

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3 votes
2 answers
61 views

Wrapping R scripts in WDL and run in docker

I am trying to run an R script as a task in WDL in a docker image. Since this is my first time working with these, I am stuck in something very simple (and in the initial stage) and am hoping somebody ...
1 vote
2 answers
126 views

Installing snakemake following official docs just won't work. Help needed

Following the docs just won't work for me. ...
3 votes
1 answer
41 views

Mounting a folder from the host to a Docker, while running it as Cromwell runtime

I have a pipeline, which is written in WDL & runs with the help of Cromwell. I use Docker...
0 votes
0 answers
30 views

How to customise options.json and config files to run WDL workflow in a remote server (not cloud)?

I am running wdl workflow (ExomeGermlineSingleSample) with Cromwell locally. Based on here (https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/), I have set "backend": "Local&...
0 votes
1 answer
59 views

Optitype for Singularity

I am trying to use optitype on an HPC without docker support or sudo privileges. A search brought me https://github.com/researchapps/optitype and https://github.com/...
1 vote
1 answer
61 views

Get Dockerfile of a bioconda package

Bioconda packages have associated containers images. E.g. bioconductor-csaw has the image quay.io/biocontainers/bioconductor-csaw...
1 vote
1 answer
319 views

Using Broad Institute RNAseq pipeline

There is a Github report for Broad's pipeline on RNA-Seq. It has a docker build file and WDL scripts. However, I don't see how any of the WDL script is being used in the docker (Dockerfile). It looks ...
1 vote
1 answer
43 views

Running tophat dockerfile in background

I need to use tophat2 to align some sequences, and I wish to use the docker container. These are large sequences so it will take a long time, plus I'm working on a university server so the chances of ...
4 votes
2 answers
974 views

Run Nextflow with file dependencies inside a Docker container?

I’m trying to run a Nextflow workflow in a custom Docker container. Without Docker, the workflow succeeds. But running it inside the container leads to an error because a dependent file cannot be ...