[FEATURE REQUEST] test submissions to all three databases
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2
- Forks
- 0
- Avg merge
- 20m
- Merged PRs (30d)
- 5
Description
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
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the seqsender-kickoff submit command and the test_data/FLU files, including the three metadata files, flu_config.yaml, and flu_sequence.fasta. Determine how the existing GenBank-only run handles submission, then define and verify a single run that processes Biosample, SRA, and GenBank and reports their submission status.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- cli, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100