Keeping bam

[ktroule]

I'm running Optitype in docker. Is there any way to keep the aligned bam to reference HLA fasta? I think its created as intermediate file, and I would like to keep it.

Not sure how to modify the config file that is in the docker image.

Thanks

[andras86]

You have to override the default config file with an additional -c parameter. Save the following into a file and supply it with -c. Make sure you reference it as a path inside the Docker container.

[mapping]
razers3=/usr/local/bin/razers3
threads=1

[ilp]
solver=cbc
threads=1

[behavior]
deletebam=false
unpaired_weight=0
use_discordant=false

[ktroule]

Thanks for the fast answer!

[ktroule]

I'm trying to get into the image to modify the config file in the image and then save it into a new image but I'm unable to do it. We've tried it different ways.

docker run -i -t fred2/optitype:latest /bin/bash

usage: OptiType [-h] --input FQ [FQ ...] (--rna | --dna) [--beta B] [--enumerate N] --outdir OUTDIR [--prefix PREFIX] [--verbose] [--config CONFIG] OptiType: error: argument --input/-i is required

Or

docker exec -it fred2/optitype:latest bash
Error: No such container: fred2/optitype:latest
Thanks

[ktroule]

Finally solved

docker run -it --entrypoint /bin/bash fred2/optitype:latest

[ktroule]

Yet another problem. Once inside I cannot modify the config.ini as I have no privileges to install apt-get install nano or other text reading tool. We the users have no way to do this as we have no control over the biodocker user.

Anyhow to modify this file?

[ktroule]

Finally managed to get into the image, modify the config.ini folder, but after commit it wont work (it does not print the usage parameters of the program).

[b-schubert]

@ktroule You don't have to manipulate the docker image at all. Just use the -c command to specify your modified config file (with the docker internal paths i.e. /data/modified_config.yml) and that should to the trick.

[ktroule]

Thanks it's finally working.