The HiGlass Server supports HiGlass and HiPiler by providing APIs for accessing and uploading tiles generated by Clodius.
Note: that the HiGlass Server itself only provides an API, and does not serve any HTML.
Prerequirements:
- Python v3
The easiest way to run HiGlass with HiGlass Server is with Docker. More information is available at higlass-docker or check out the Dockerfile.
To install HiGlass Server manually follow the steps below. Note we strongly recommend to create a virtual environment using Virtualenvwrapper for example. Skip step 2 if you don't work with virtual environments.
git clone https://github.com/hms-dbmi/higlass-server && cd higlass-server
mkvirtualenv -a $(pwd) -p $(which python3) higlass-server && workon higlass-server
pip install --upgrade -r ./requirements.txt
pip install --upgrade -r ./requirements-secondary.txt
python manage.py runserverAlthough there is an API endpoint for uploading files, but it is more direct to use a manage.py script:
COOLER=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool
HITILE=wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile
wget -P data/ https://s3.amazonaws.com/pkerp/public/$COOLER
wget -P data/ https://s3.amazonaws.com/pkerp/public/$HITILE
python manage.py ingest_tileset --filename data/$COOLER --filetype cooler --datatype matrix --uid cooler-demo
python manage.py ingest_tileset --filename data/$HITILE --filetype hitile --datatype vector --uid hitile-demo
We can now use the API to get information about a tileset, or to get the tile data itself:
curl http://localhost:8000/api/v1/tileset_info/?d=hitile-demo
curl http://localhost:8000/api/v1/tiles/?d=hitile-demo.0.0.0
Start the server:
python manage.py runserver localhost:8001
// or
npm start
Test the server:
./test.sh
// or
npm test
Bump version of server:
bumpversion patch
Update source code:
./update.sh
pybbi installation fails on macOS: Check out nvictus/pybbi#2
The code in this repository is provided under the MIT License.