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Questions tagged [docker]

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

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How do I mount resource directories into my docker image via Cromwell / WDL?

Problem is that the docker image i am trying to run requires a mount points to several resources in order to run. Example: ...
bio-X's user avatar
  • 21
1 vote
2 answers
101 views

How to run a GATK Docker Image with local files?

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command: ...
rimo's user avatar
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1 vote
1 answer
300 views

How to pack up a Python script in the form a Dockerfile

I have a simple Python script with this header ...
Zizogolu's user avatar
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2 votes
1 answer
56 views

Importing local files to a GATK docker image

I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file My OS version ...
Zizogolu's user avatar
  • 2,232
2 votes
1 answer
212 views

Singularity & GATK 4.4.0.0. CreateSequenceDictionary

I ran the following code in bash (I added print statements for ease): ...
Indira's user avatar
  • 380
2 votes
1 answer
132 views

Why might parabricks not be writing output to the output file I provided?

This feels like a silly question, but I am testing parabricks bammetrics and nothing is being written to my output file. This is the command I am using: ...
womy's user avatar
  • 23
4 votes
2 answers
436 views

ERR: error while loading shared libraries: libjulia.so.1: cannot open shared object file [Julia] - Ubuntu 22.04

I'm trying to build a Dockerfile. It has a tool called Atria that utilizes Julia. Since Ubuntu 22.04 does not have Julia package, I had to resort to installing it. The following is the Dockerfile: <...
pubsurfted's user avatar
1 vote
0 answers
94 views

Feeding the output of one task into another in WDL

Hi there I'm new to WDL and I need to complete a two-step workflow, Basically, what I need to do is to extract and merge two reads dataset (forward and reverse) for a sample and pass the merged, ...
Matteo's user avatar
  • 121
1 vote
0 answers
66 views

Implement a WDL workflow for a docker container I built

I start saying my background is Biology and I'm totally new to WDL, so I'm aware my code will be messy but I'm trying to learn. My problem is, essentially, to run a Docker container I built and tested ...
Matteo's user avatar
  • 121
3 votes
2 answers
489 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 ...
binn's user avatar
  • 73
2 votes
1 answer
417 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...
crusher083's user avatar
1 vote
2 answers
544 views

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

Following the docs just won't work for me. ...
titus's user avatar
  • 131
2 votes
1 answer
136 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...
mox's user avatar
  • 333
0 votes
1 answer
138 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/...
SophistRS's user avatar
1 vote
1 answer
52 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 ...
Siddharth Kurkure's user avatar
4 votes
2 answers
2k 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 ...
Konrad Rudolph's user avatar
1 vote
1 answer
373 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 ...
SmallChess's user avatar
  • 2,729