/gemini-playground

opinionated scripts to managed multiple nextflow based gemini-loading, spawn gemini session for playaround wit query

Primary LanguageShell

Gemini Playground

Containerized Style playground. Required only Docker and time waiting when first time spawn session.
opinionated scripts to managed multiple nextflow based gemini-loading, spawn gemini session(web) for playaround wit query

Prerequisite

Usage (Exploration & Investigation mode)

  • clone this repository to your machine 
    git clone https://github.com/sinonkt/gemini-playground.git
cd gemini-playground
mkdir -p data/dbs
  • get portable database files (eg. test.db, joint.db, g1k.db), which ready for query, from lab members.
  • then move db files to ./data/dbs directory, we just created.
  • start gemini web interface at rootDir of gemini-playground 
    ./bin/spawn-gemini-web.sh ${your_interested_db_name}.db    # for example g1k.db
  • browse web at http://localhost:8080
  • when you are done with your exploration. 
    ./bin/stop-gemini.sh

***Notes, Builtin module is not available on web interface. So
***For hardcore user, you can spawn gemini session then query inide docker container directly.

./bin/spawn-gemini.sh

then you will be inside docker container, where you can run cmd like this.

gemini query -q "select chrom, start, end, ref, alt, (gts).(*) from variants" /dbs/joint.db

Querying

we can skip all installation/preprocessing section in Gemini Doc