kapsakcj / sneakernet Goto Github PK

Is your feature request related to a problem? Please describe.
Docker image for SneakerNet is pretty large due to the 4GB minikraken database being included with it. Removing it would reduce the image size by 1/2.

Currently users are forced to use the included minikraken db instead of being allowed to supply their own kraken database. This would allow for flexibility and users could use whatever kraken1 database they want.

Describe the solution you'd like
dockerfile changes:

• line 270: sed -i 's+/opt/kraken/full-20140723+/kraken-database+g' config/settings.conf && \
• line 271: mkdir /data /kraken-database
• delete lines 276-276

Will also need to provide users instructions on how to use their own kraken1 database with a container (both singularity and docker). Something along the lines of:

docker run -v /user-krakenDB:/kraken-database lskatz/sneakernet:latest […]

singularity exec -B /user-krakenDB:/kraken-database sneakernet.simg [...]

Additional context
Add any other context or screenshots about the feature request here.