Containerised gene search

An Apache server that reverse proxies to an elasticsearch instance with indexes built from ensembl data. The indexes are built with shusson/genesearch

Why

We wanted to be able to host our own gene search service as any existing services did not meet our requirements.

Elasticsearch provides nice search functionality and comes with a REST API baked in. Easy to populate with ensembl data and it is free.

We added apache as a simple security layer in front of elasticsearch. The apache configuration only allows specific requests to be proxied to elasticsearch and enables SSL. See apache/conf/httpd-ssl.conf

Usage

git clone https://github.com/shusson/docker-bouncy.git

Add SSL files to apache/ssl, apache is configured for:

• org.crt
• org.key
• org.pem
• org-ca.pem

docker-compose up -d

Wait a moment for the servers to initialise then make a query

curl -XGET 'https://localhost/_elasticsearch/_search?pretty' -d'
{
    "query": {
        "match_phrase_prefix" : {
            "symbol" : {
                "query" : "REST"
            }
        }
    }
}'

Apache logs will be written to logs directory

Note

Elastic search may require extra setup on certain VMs

sudo sysctl -w vm.max_map_count=262144