search

niaid / image_portal_workflows

Workflows related to project previously referred to as "Hedwig"
BSD 3-Clause "New" or "Revised" License
5 stars 1 forks source link

Add Dockerfile for bioformats2raw #280

Closed annshress closed 1 year ago

annshress commented 1 year ago

Add Dockerfile for bioformats2raw

Next: Setup an environment with imod binaries.

blowekamp commented 1 year ago

@philipmac There are some unmaintained Docker files in the "em_workflows/utils" directory. Should this go there as well or is a refactor needed?

mbopfNIH commented 1 year ago

The bioformats2raw via docker runs without errors on my M1 Mac, but I have no way to test the validity of the Zarr output.

mbopfNIH commented 1 year ago

Using WGET makes this Dockerfile more self-contained, but will require a longer start-up time. Is there a way to just run bioformats2raw once the container has been created?

And should it use ubuntu or rocky?

annshress commented 1 year ago

@mbopfNIH COPY or WGET will only affect the docker image building time. wget replaces the manual hassle of downloading the binary. Once the image is built, container will have bioformats2raw binary available.

Eventually, the base image should be changed to rocky to somewhat replicate the remote server.

annshress commented 1 year ago

Closing this PR, as docker branch (https://github.com/niaid/image_portal_workflows/pull/284) has been merged which contains this commit.