lskatz
commented
2 years ago Thank you so much for your effort! I have pulled in the documentation which should be very helpful to the community @kapsakcj
Closed kapsakcj closed 2 years ago
lskatz
commented
2 years ago Thank you so much for your effort! I have pulled in the documentation which should be very helpful to the community @kapsakcj
This PR adds install & usage instructions for conda, docker, and singularity. I also altered the formatting of some headings for readability. You can view the rendered markdown on my fork: https://github.com/kapsakcj/datasets-sars-cov-2
To test, I used the following versions though relatively recent versions of all should work properly. Except maybe Singularity 2.x.x, don't even bother trying - it's not worth it.
Singularity was the oddball, as per usual, since it auto-mounts your home drive
/home/curtis_kapsakand sets it it as $HOME by default. You have to trick the container into thinking$HOME=/home/userdue to the vdb-config/sra-toolkit workaround that Kelsey implemented in the StaPH-B docker image. It won't run without it.I tested out the StaPH-B container just now and previously, if you'd like to see some of the output of
GenFSGopher.pl. Fastq files downloaded properly & checksums looked good. I've successfully downloaded all 6 datasets using the Staph-B docker image.Also removed the TravisCI badge since Travis-ci.org is dead & it pointed to a different repo anyways (globalmicrobialidentifier-WG3/datasets)
Please feel free to test and/or suggest changes to this PR.
Big thank you to @rpetit3 for adding this to bioconda and @k-florek for creating the StaPH-B docker image! This wouldn't be possible without them đź‘Ź