fastq_dump.cwl might have some problems when running without Internet connection

[michael-kotliar]

It looks like fastq_dump.cwl might have some problems when running without Internet connection. fastq-dump downloads something even when extracting data from the previously downloaded sra file.

[michael-kotliar]

Update Dockerfile to have all the required data within a container
https://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/

[medcelerate]

How big does this make the container?

[michael-kotliar]

Huge! I didn't check it before submitting this issue :) Maybe we can provide it as an input directory if necessary.

[medcelerate]

That sounds like a good approach. Does fastq_dump require a directory in a specific location or is there a flag that can be passed in.

[michael-kotliar]

It's not a flag, but it can be configured to any location when building an image. By default, it should be at /ncbi/public

[mr-c]

@michael-kotliar Can you work with the biocontainers.pro people so that their container has the offline functionality (and then switch us to using their container)?

https://biocontainers.pro/#/tools/sra-toolkit
https://hub.docker.com/r/biocontainers/sra-toolkit
https://github.com/BioContainers/containers/tree/master/sra-toolkit