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CDCgov / seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
https://cdcgov.github.io/seqsender/
Apache License 2.0
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There is no submission directory at /home/user1/FLU_reporting #47

Closed SeanSierra-Patev closed 5 months ago

SeanSierra-Patev commented 5 months ago

This may be an extremely simple question, I'm probably overlooking something to do with docker, but I'm trying a test submission via Docker, the command (and response) being

`docker exec -it seqsender bash seqsender-kickoff submit --organism FLU -bsn --submission_dir /home/user1/FLU_reporting/ --submission_name test_sub --config_file config.yaml --metadata_file metadata.csv --fasta_file RI-M04353-2024013.fasta --test

There is no submission directory at /home/user1/FLU_reporting `

the path is correct, my submission folder "test_sub" is indeed at /home/user1/FLU_reporting/

I'm at a loss

SeanSierra-Patev commented 5 months ago

Oh nevermind, it was an issue with how I was invoking docker to begin with