Young

Closing this PR until the Vibrio database is updated

This is finally ready for review! I needed to tag keras and tensorflow to a specific version.

This means there are more differences in the dockerfiles: ``` $ diff genomad/1.7.4/Dockerfile genomad/1.7.5/Dockerfile 2c2 < ARG GENOMAD_VER="1.7.4" --- > ARG GENOMAD_VER="1.7.5" 4a5,6 > ARG KERAS_VER="2.15.0" > ARG TENSORFLOW_VER="2.15.0" 18c20...

Version 1.7.6 came out, so I've updated all the files in this PR. There's nothing really new about this version. It's more for package managers to ensure that the version...

Version 1.8.0 came out. In addition the the features introducted in 1.7.5, there is now > Added the --min-number-genes parameter to the summary module. This parameter allows users to set...

The documentation in the readme uses `snpeff` Link to documentation : https://github.com/StaPH-B/docker-builds/tree/master/snpeff/5.2a

I'm not familiar with using snpeff, but you should be able to build your own database. You will need to mount (docker) or bind (singularity) your directory (like `/blue/bphl-florida/dongyibo/snpeff_database`) to...

Version 2.0.5 came out, so I updated the files to the current version.

From what I gather, it looks like Docker prevented numactl from setting mempolicy. https://forums.docker.com/t/cannot-run-numactl-interleave-all-in-docker/40631/5

I am encountering problems with the biocontainer image as well (quay.io/biocontainers/masurca:4.1.1--pl5321hb5bd705_0): ``` # masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz Verifying PATHS... jellyfish OK runCA OK createSuperReadsForDirectory.perl OK creating script...