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https://github.com/higlass/higlass-server
Server component for HiGlass that manages and serves tiled data
https://github.com/higlass/higlass-server
gehlenborglab hi-c higlass
Last synced: about 2 months ago
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Server component for HiGlass that manages and serves tiled data
- Host: GitHub
- URL: https://github.com/higlass/higlass-server
- Owner: higlass
- License: mit
- Created: 2016-10-13T18:28:20.000Z (over 8 years ago)
- Default Branch: develop
- Last Pushed: 2023-05-23T02:03:39.000Z (over 1 year ago)
- Last Synced: 2024-04-24T11:05:25.541Z (9 months ago)
- Topics: gehlenborglab, hi-c, higlass
- Language: Python
- Homepage:
- Size: 125 MB
- Stars: 17
- Watchers: 18
- Forks: 19
- Open Issues: 54
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# HiGlass Server
The HiGlass Server supports [HiGlass](https://github.com/higlass/higlass) and [HiPiler](https://github.com/flekschas/hipiler)
by providing APIs for accessing and uploading tiles generated by
[Clodius](https://github.com/higlass/clodius).
[](http://higlass.io)
[](API.md)
[](https://doi.org/10.5281/zenodo.1308945)
_Note: that the HiGlass Server itself only provides an API, and does not serve any HTML._
## Installation
**Prerequirements**:
- Python `>=v3.6`
### Docker
The easiest way to run HiGlass with HiGlass Server is with Docker. More information is available at [higlass-docker](https://github.com/higlass/higlass-docker#readme) or check out the [Dockerfile](docker-context/Dockerfile).
This project also includes a Dockerfile in the docker-context directory that can be used to run a locally checked out copy of higlass-server as follows:
```bash
docker build -t higlass-server -f docker-context/Dockerfile .
docker run -d --cap-add SYS_ADMIN --device /dev/fuse --security-opt apparmor:unconfined --name higlass-server higlass-server
```
### Manually
To install HiGlass Server manually follow the steps below. Note we strongly recommend to create a virtual environment using [Virtualenvwrapper](https://pypi.python.org/pypi/virtualenvwrapper) for example. Skip step 2 if you don't work with virtual environments.
```bash
git clone https://github.com/higlass/higlass-server && cd higlass-server
```
#### Manually with virtualenvwrapper
```bash
mkvirtualenv -a $(pwd) -p $(which python3) higlass-server && workon higlass-server
pip install --upgrade -r ./requirements.txt
python manage.py migrate
python manage.py runserver
```
#### Manually with conda
```bash
conda env create -f environment.yml
conda activate higlass-server
python manage.py migrate
python manage.py runserver
```
To enable the register_url api endpoint, HiGlass depends on a project called httpfs to cache external url files. Tests depend on this process running. Set it up as follows:
```bash
pip install simple-httpfs
mkdir -p media/http
mkdir -p media/https
simple-httpfs media/http
simple-httpfs media/https
```
Or simply use `./unit_tests.sh`.
---
## Uploading Files
Although there is an API endpoint for uploading files, but it is more direct to use a `manage.py` script:
```
COOLER=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool
HITILE=wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile
wget -P data/ https://s3.amazonaws.com/pkerp/public/$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
```
---
## Development
**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
```
## Troubleshooting
**pybbi installation fails on macOS**: Check out https://github.com/nvictus/pybbi/issues/2
### macOS 10.15 dependencies
- `brew install hdf5`
- `brew install libpng`
- `brew install jpeg`
- [FUSE for Mac](https://osxfuse.github.io/)
## License
The code in this repository is provided under the MIT License.