Is this feature for general SeqSender usage or for submitting to a specific database, if so what database?
I am trying to test the pipeline for all three databases (with flu) but there are three separate metadata files for each biosample, sra, and genbank.
Is your feature request related to a problem? If so please describe.
I have successfully run a test for genbank only but hoping to confirm all three databases can be successfully submitted to in one run. Please let me know if I am missing something!
this command successfully generated files for Genbank but didn't actually submit
docker run --rm -v $PWD/test_data/FLU/:/data seqsender bash /seqsender/seqsender-kickoff submit --genbank --organism FLU --submission_name 0807test --submission_dir /data --config_file /data/flu_ config.yaml --metadata_file /data/flu_genbank_metadata.csv --fasta_file /data/flu_sequence.fasta
I then ran this and it submitted via FTP
docker run --rm -v "$PWD/test_data/FLU:/data" seqsender bash /seqsender/seqsender-kickoff submission_status --submission_name 0807test --submission_dir /data
Is this feature for general SeqSender usage or for submitting to a specific database, if so what database?
I am trying to test the pipeline for all three databases (with flu) but there are three separate metadata files for each biosample, sra, and genbank.
Is your feature request related to a problem? If so please describe.
I have successfully run a test for genbank only but hoping to confirm all three databases can be successfully submitted to in one run. Please let me know if I am missing something!
this command successfully generated files for Genbank but didn't actually submit
docker run --rm -v $PWD/test_data/FLU/:/data seqsender bash /seqsender/seqsender-kickoff submit --genbank --organism FLU --submission_name 0807test --submission_dir /data --config_file /data/flu_ config.yaml --metadata_file /data/flu_genbank_metadata.csv --fasta_file /data/flu_sequence.fastaI then ran this and it submitted via FTP
docker run --rm -v "$PWD/test_data/FLU:/data" seqsender bash /seqsender/seqsender-kickoff submission_status --submission_name 0807test --submission_dir /data