https://github.com/slaclab/cryosparc-docker
Docker wrapper for cryosparc
https://github.com/slaclab/cryosparc-docker
Last synced: about 1 year ago
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Docker wrapper for cryosparc
- Host: GitHub
- URL: https://github.com/slaclab/cryosparc-docker
- Owner: slaclab
- Created: 2018-09-19T06:09:21.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-10-22T03:45:21.000Z (over 1 year ago)
- Last Synced: 2025-03-28T04:27:17.586Z (about 1 year ago)
- Language: Shell
- Size: 50.8 KB
- Stars: 7
- Watchers: 6
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# docker image for cryosparc v2
You first need to obtain a license for cryosparc via https://cryosparc.com/download/ and cat it into a location that so that the docker build process can pick it up:
```
export CRYOSPARC_LICENSE_ID=
make license
```
All this really does is to put it into a text file under .secret.
Then to actually build the image:
```
make build
```
You can change the version to be installed via environment variables, eg to install
```
CRYOSPARC_VERSION=4.4.0 CRYOSPARC_PATCH=231114 make build
```
Developer
===
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.