docker container for Pindel

Question

[genya35]

Hello,

Could a kind a person please create a docker container for Pindel and post it on Docker Hub. The dockerfile is found here: https://hub.docker.com/r/mgibio/pindel/~/dockerfile/

I can't find an active container and a firewall on my machine is preventing the creation of my own.

Thank you

[vimalkvn]

The image on Docker hub doesn't have the latest tag which docker pull looks for by default. The only available version is tagged v0.2.5b8. You should be able to pull it using:

docker pull mgibio/pindel:v0.2.5b8

[genya35]

Thanks, your suggestion worked. Could you please suggest how to run pindel and pindel2vcf via docker?

I've tried this:

my $cmd1 = `docker run -v /home/yey/mdl3:/data --rm mgibio/pindel:v0.2.5b8 /opt/pindel-0.2.5b8/pindel \
   -f /data/reference/chr4.fa \
   -i /data/pindel/bam_files.txt \
  -c ALL -o /data/pindel/Output`; print $cmd1;

I get an error message :

unknown argument: /opt/pindel-0.2.5b8/pindel
Pindel version 0.2.5b8, 20151210.
Required parameter -f/--fasta the reference genome sequences in fasta format needs to be set.

Thank you

[vimalkvn]

No problem! /opt/pindel-0.2.5b8/pindel argument isn't required as it appears pindel is run by default when starting the container. Looks like pindel2vcf is a separate Docker image https://hub.docker.com/r/mgibio/pindel2vcf