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fastq_dump.cwl might have some problems when running without Internet connection #36
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Update Dockerfile to have all the required data within a container |
How big does this make the container? |
Huge! I didn't check it before submitting this issue :) Maybe we can provide it as an input directory if necessary. |
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. |
It's not a flag, but it can be configured to any location when building an image. By default, it should be at |
@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 |
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.
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