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abaizan / kodoja

Kodoja: identifying viruses from plant RNA sequencing data
MIT License
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kodoja_build.py test changes #14

Closed peterjc closed 6 years ago

peterjc commented 6 years ago

The goal of this pull request is to remove the special --test switch in kodoja_build.py and run the tests via the public command line API instead.

peterjc commented 6 years ago

This will need a minor update if #13 is merged first.

peterjc commented 6 years ago

Rebasing for merge conflict...

peterjc commented 6 years ago

While working on this I found a couple of minor issues, fixed via #21.

peterjc commented 6 years ago

I was seeing FTP errors with ftp://ftp.ncbi.nih.gov/genomes/refseq/viral/assembly_summary.txt which were resolved by switching to HTTPS.

Instead started seeing errors later with ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.tsv

Update: Should be solved by 2c6a625cefed28e8511a702b8e95f18035f790a0 cross reference https://bugs.python.org/issue27973