vcf2maf does not seem to have all files required to run

[D0g4]

I am an enthusiast of this whole concept of BioContainers, and yet very new to it (and dockers as well). So, this issue might likely be because I am missing something. When I try to to run the command vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf, just to test whether it is working, I get the message:

ERROR: Provided --input-vcf is missing or empty: tests/test.vcf

And if I skipped this step and jump right at my own files, say: vcf2maf.pl --input-vcf Exom1_somatic.vcf --output-maf Exom1_somatic.vcf.maf

The following message appears: ERROR: Provided --ref-fasta is missing or empty: /root/.vep/homo_sapiens/95_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz

Note: this vcf2maf package depends on VEP to run, which also contains the reference files.

So, my question is: where are those files, or the VEP package within the vcf2maf container? Is there anything I am missing here?

Any help is very much appreciated! Thanks!

[osallou]

Hi, this is a conda based container (@bgruening). for your first command, tests file are not present in container. To execute cmd against your files, they must be mounted in container with the "-v host_path:container_path" option.

I do not know this tool and usage, but seems it needs some reference data (VEP). Those data are not either in container. You should make them available in the same way.

1. download reference data
2. mount dir where data is available in container
3. specify path to reference data with the --ref-fasta option

[D0g4]

Hi @osallou, Thank you for the quick follow-up. I pulled the docker image from [here](docker pull quay.io/biocontainers/vcf2maf:1.6.17--pl526hdbffeaa_0).

I guess that was my main concern: the files not being there at all. Which raises a new question: does it mean that I have to install the VEP package (which contains those files) separately? If so, I believe I am missing the core understanding of containers: isn't the idea behind it so one can use/pull a container from a given package, which should already contain all dependencies?

Any light shed on it is much appreciated. And thanks again for the reply!

[osallou]

container contain software and its dependencies, but not data.

container size is limited, as such, data should be made available by user in container.

If some software is missing from VEP to use vcf2maf, then you should create an issue in bioconda related software (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/vcf2maf) If only VEP data is needed, then you should download it and mount it in container