Name: infino-docker
Owner: Hammer Lab
Description: Development environment for infino.
Created: 2017-08-23 18:55:02.0
Updated: 2017-08-23 18:55:44.0
Pushed: 2018-01-11 06:04:55.0
Homepage: null
Size: 17
Language: Shell
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This is a development environment for infino.
git clone git@github.com:hammerlab/immune-infiltrate-explorations.git
sudo mkdir -p /data/modelcache_new && sudo chmod -R 777 /data/modelcache_new
docker pull hammerlab/infino-docker:latest
docker run -d --name [name your container here] -v $HOME/immune-infiltrate-explorations:/home/jovyan/work -v /data/modelcache_new:/modelcache -v /data/output_unpackaged:/data:ro -v /data/microarray:/microarrays:ro -v /data/cibersort:/cibersort:ro -p [put port that you have forwarded here]:8888 --user root -e NB_UID=$(id -u) -e NB_GID=$(id -g) hammerlab/infino-docker:latest
git
from the host (as opposed to from inside the docker container).This command mounts your personal code directory, the shared model cache, the shared RNA-seq and microarray data directories, and the global Cibersort install, and acts as your user account for all editing purposes. (Note: anything mounted into /home/jovyan
will have its ownership changed, which isn't possible in some situations, e.g. if readonly file system.)
You can view logs with: docker logs [name of your container here]
.
You can get a shell into the container in the following ways:
docker run -it --name [name your container here] -v $HOME/immune-infiltrate-explorations:/home/jovyan/work -v /data/modelcache_new:/home/jovyan/modelcache -p [put port that you have forwarded here]:8888 --user root -e NB_UID=$(id -u) -e NB_GID=$(id -g) hammerlab/infino-docker:latest bash
(if you are starting a new container)docker exec -it [name your container here] bash
(shell into an existing container)Teardown:
er stop [name of your container here] # restart with "docker start"
er rm [name of your container here]
Mounted directories will be unaffected because they live on the host.
This is derived from the Jupyter “data science notebook” image:
You can use any options from that image, e.g. you can grant sudo access by adding -e GRANT_SUDO=yes
.
Our image installs pip and conda requirements from the primary repository into a python3 environment. Here is how to get those if you want to update the image:
https://raw.githubusercontent.com/hammerlab/immune-infiltrate-explorations/master/model-single-origin-samples/biokepi/conda_requirements.txt
https://raw.githubusercontent.com/hammerlab/immune-infiltrate-explorations/master/model-single-origin-samples/biokepi/pip_requirements.txt
To build: docker build -t hammerlab/infino-docker:latest .