docker compose up
to start the robin docker
docker run -it -v $(pwd):$(pwd) -w $(pwd) -p 8086:8086 -p 8889:8888 robin
to run the api:
docker run --detach
--publish 8888:80
--volume ~/hg-data:/data
--volume ~/hg-tmp:/tmp
--name higlass-container
higlass/higlass-docker
npm run start-api-worker
Note: this will be fixed when I care enough to fix it. but for now running 3 more commands to set up npm is not bad.
I had to rewrite a chunk of higlass to get it to run with react 18, as such it is included as part of the project rather than a module.
it has its own dependancies and you need to run npm clean-install from inside /src/components/visualizationTools/HiGlass/higlass to install its dependancies
it is included as a submodule, run git submodule update --init --recursive the first time you clone the repo to clone it.
then just git submodule update --init --recursive ./src
Note: this project uses craco to override a few webpack configs of create react app. find them in craco.config.js,
webpack.config.js and tsconfig.json are not used.
For higlass to interact with our data we need to first upload it to the higlass server, thus we can start a higlass server with
docker pull higlass/higlass-docker # Ensure that you have the latest.
docker run --detach
--publish 8888:80
--volume ~/hg-data:/storage/store/Robin_ComprehensiveLoopCaller/data/higlassTracks/
--volume ~/hg-tmp:/storage/store/Robin_ComprehensiveLoopCaller/data/higlassTempData/
--name higlass-container
higlass/higlass-docker
or my provided startHiglassserver.sh script in this folder
to upload a track
first check if its there:
docker exec higlass-container ls /tmp
then upload it
docker exec higlass-container python higlass-server/manage.py ingest_tileset --filename /tmp/test.txt --filetype vector --datatype vector
higlass-manage ingest --filetype vector --datatype vector ./test.txt