updating the emmtyper blast database #1084
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There is NOT a new version of emmtyper, but there ARE new emmtypes.
I use emmtyper for Group A Strep isolates (often S. pyogenes). I noticed awhile ago (MDU-PHL/emmtyper#21 (comment)) that there did not seem to be an easy way to update the fasta file used for the emm types. @Daniel-VM has created a script just for this problem at https://github.com/Daniel-VM/cdc-utilities, which I thought might be useful to add to the image.
I, therefore, took the original emmtyper Dockerfile, updated the base micromamba image to 1.5.8, simplified the lines, add a CMD line, and added in some lines to use emm_download_makedb.py to download the most-recent files.
I also updated the corresponding README.md
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15
)spades/3.12.0/Dockerfile
)shigatyper/2.0.1/test.sh
)spades/3.12.0/README.md
)