gosling-higlass-https-server-setup

This repository describes a way to setup a HTTPS HiGlass server using a free Let's Encrypt service. This allows to fetch tiles from a HiGlass server (e.g., https://server.gosling-lang.org) in HTTPS clients (e.g., https://gosling.js.org). Because of the security issue, you cannot fetch tiles if the server is not HTTPS server but the client is HTTPS.

ssh to the server

ssh -i gosling.pem [email protected]

Setup

Reference: https://medium.com/@pentacent/nginx-and-lets-encrypt-with-docker-in-less-than-5-minutes-b4b8a60d3a71

Place a nginx config file to a certain directory:

$ mv hgserver_nginx.conf webcontext/sites-enabled/hgserver_nginx.conf
$ ls
init-letsencrypt.sh     docker-compose.yml      web-context

Run init-letsencrypt.sh

This will run certbot which will validate your site and give certificates for HTTPS.

./init-letsencrypt.sh

If you recived a "success" message, you are all set!

Let's start the server

sudo docker-compose up

Adding Tilesets

Reference: https://github.com/higlass/higlass-docker

Download a tileset data to add

$ sudo wget -P /data/hg-tmp/ http://YOUR_LINK.COM

Confirm that a tileset is visible in Docker

$ sudo docker exec higlass-container ls /tmp

Cistrome.H3K27ac.ChIP-seq.multires.mv5
...

Ingest a tileset:

$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
      --filename /tmp/Cistrome.H3K27ac.ChIP-seq.multires.mv5 \
      --filetype multivec \
      --datatype multivec \
      --project-name "gosling-data-v1" \
      --uid cistrome-multivec \
      --coordSystem hg38
      
$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
      --filename /tmp/hg38.chrom.sizes \
      --filetype chromsizes-tsv \
      --datatype chromsizes \
      --coordSystem hg38 \
      --uid hg38
      
$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
      --filename /tmp/Leung2015_Aorta.hg38.mapq_30.1000.mcool \
      --uid leung2015-hg38 \
      --filetype cooler \
      --datatype matrix

$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
      --filename /tmp/Olig2.5k_interactions_ucsc_genome_browser.inter.bb \
      --filetype bigbed \
      --datatype bedlike \
      --uid oligodendrocyte-plac-seq-bedpe 

$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
    --filename /tmp/gwas.bed.beddb \
    --filetype beddb \
    --datatype bedlike \
    --uid gwas-beddb
    
$ sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset \
    --filename /tmp/gene-mm10.beddb \
    --filetype beddb \
    --datatype gene-annotation \
    --uid gene-annotation-mm10 \
    --coordSystem mm10

Restart Docker

sudo docker-compose down && sudo docker-compose pull && sudo docker-compose up

To Show Docs

docker exec -i higlass-container sed -i 's/HGAC_HOMEPAGE_DEMOS=false/HGAC_HOMEPAGE_DEMOS=true/' higlass-app/config.js