Questions tagged [docker]
Docker is a computer program that performs operating-system-level virtualization, also known as "containerization".
19 questions
1 vote
1 answer
43 views
Installing old version of DESeq2
I am trying to install old version of DESeq2 (2019) and used the Dockerfile below: ...
- 205
3 votes
1 answer
151 views
Low Memory Usage with DeepVariant
I am running DeepVariant on a c5.4xlarge instance on AWS EC2 with Ubuntu Server 24.04. I'm using htop to monitor my CPU and memory usage. During make_examples, I noticed that only 8GB of my 32GB of ...
- 33
2 votes
0 answers
38 views
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: ...
- 21
2 votes
2 answers
236 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: ...
- 1,063
1 vote
1 answer
458 views
How to pack up a Python script in the form a Dockerfile
I have a simple Python script with this header ...
- 2,242
2 votes
1 answer
99 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 ...
- 2,242
2 votes
1 answer
239 views
Singularity & GATK 4.4.0.0. CreateSequenceDictionary
I ran the following code in bash (I added print statements for ease): ...
- 380
2 votes
1 answer
203 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: ...
- 85
4 votes
2 answers
505 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: <...
- 383
1 vote
0 answers
126 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, ...
- 121
1 vote
0 answers
88 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 ...
- 121
3 votes
2 answers
597 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 ...
- 73
2 votes
1 answer
485 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...
- 23
1 vote
2 answers
624 views
Installing snakemake following official docs just won't work. Help needed
Following the docs just won't work for me. ...
- 131
2 votes
1 answer
173 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...
- 343