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[Request An Update]: kaptive 2.0.7 + V. parahaemolyticus databases #661

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kapsakcj opened this issue May 3, 2023 · 4 comments · May be fixed by #694
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[Request An Update]: kaptive 2.0.7 + V. parahaemolyticus databases #661

kapsakcj opened this issue May 3, 2023 · 4 comments · May be fixed by #694
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enhancement New feature or request

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@kapsakcj
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kapsakcj commented May 3, 2023

What container needs an update?

upgrade to kaptive 2.0.7 and add capability to serotype V. parahaemolyticus using newly-released databases

original tweet that I saw: https://twitter.com/DrKatHolt/status/1653795878077968386

publication: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001007

github repo for where V. parahaemolyticus databases live: https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping

would be good to also add a test to the test stage that downloads a V. parahaemolyticus genome and runs kaptive on it with the new databases
@kapsakcj kapsakcj added the enhancement New feature or request label May 3, 2023
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kapsakcj commented May 3, 2023

also note that the github organization for Kaptive has changed - this will need to be taken into account when writing the dockerfile:

https://github.com/klebgenomics/Kaptive/releases

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kapsakcj commented May 3, 2023

Started a dev branch cjk-kaptive-upgrade with the dockerfile & README.md in progress

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kapsakcj commented May 4, 2023

dockerfile is in a stable place, don't think I have many more changes to make. the docker image builds successfully and tests against K.pneumo, A.baum, and Vparahaem

Last piece is to add information on the custom database to /kaptive/2.0.7/README.md

@kapsakcj kapsakcj mentioned this issue Jul 21, 2023
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Opened PR #694 to address this issue

@erinyoung erinyoung mentioned this issue Sep 6, 2023
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@erinyoung erinyoung mentioned this issue Jan 11, 2024
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add kaptive 2.0.7 & custom Vibrio parahaemolyticus serotyping db, take 2 StaPH-B/docker-builds
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@kapsakcj @erinyoung