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cryosparc-docker's Introduction

docker image for cryosparc v2

You first need to obtain a license for cryosparc via https://cryosparc.com/download/

build with your license key from cryosparc:

export CRYOSPARC_LICENSE_ID=<BLAH>
docker build --build-arg CRYOSPARC_LICENSE_ID=${CRYOSPARC_LICENSE_ID} . -t slaclab/cryosparc-docker:2.2.0

run (for testing) via

docker run -e CRYOSPARC_LICENSE_ID=${CRYOSPARC_LICENSE_ID} \
    -e JUPYTERHUB_USER=ytl -e EXTERNAL_UID=7017 \
    -e EXTERNAL_GROUPS=sf:1051,cryo-data:3591,bd:1124 \
    -e HOMEDIRS=/gpfs/slac/cryo/fs1/u/ \
    -v /gpfs/slac/cryo/fs1/u/ytl/cryosparc-v2/:/gpfs/slac/cryo/fs1/u/ \
    -v /gpfs/slac/cryo/fs1/exp/:/gpfs/slac/cryo/fs1/exp/ \
    -v /scratch:/scratch \
    -p 39000:39000 -p 39001:39001 -p 39002:39002 -p 39003:39003 -p 39004:39004 \
    slaclab/cryosparc-docker:2.2.0

notes

  • to enable access to file storage, the container will drop privs to that defined by JUPYTERHUB_USER, EXTERNAL_UID and EXTERNAL_GROUPS.

cryosparc-docker's People

Contributors

yee379 avatar

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