gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

MIT License

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Prepare Docker container with MATLAB runtime #18

Closed agitter closed 4 years ago

agitter commented 5 years ago

16 confirmed that it is possible to run SINGE inside a Docker to container using compiled MATLAB code. Our next step will be to create a general purpose SINGE Docker container. Specific tasks include:

[x] Create a command line interface #17
[x] Release a new version of SINGE
[x] Compile that new release and host it somewhere stable
[ ] ~Remove the temp versions of SINGE at https://www.biostat.wisc.edu/~gitter/tmp/~
[x] Create a Docker container using the strategy in #16 and the new release

agitter commented 5 years ago

CHTC shared the Docker command that HTCondor runs after transferring files, pulling a Docker container, and starting the container: docker run --user $(id -u):$(id -g) -v $PWD:/scratch -w /scratch username/imagename:tag /path/to/executable

OSG uses Singularity and has a related command: https://gist.github.com/ChristinaLK/3e147f940cd02513c4cdc7c4b04ccfed

We could test these using the compiled SCINGE_Example from #16 while we work on the more general container.

agitter commented 4 years ago

Closed by the v0.4.0 release. We now have a process for pushing temporary compiled MATLAB executables to https://www.biostat.wisc.edu/~gitter/tmp (or some other temporary location) and using them in temporary Docker images. When the code is versioned, we upload the versioned executables to the GitHub release. Then we create a new versioned Docker image from those versioned executables, which is visible from https://hub.docker.com/r/agitter/singe/tags