igo-qc

Contents

• Description
• Development Steps
• Deployment Steps

Description

Site displaying run statistics of sequencing projects (E.g. GATK Picard, Cell Ranger, etc.).

Features

• Pulls data from LIMS and ngs-stats to visualize in grid and graphs
• Allows users to reset qc-status of runs

Development Notes

After setting up Mongo, Backend, & Frontend (in that order), the igo-qc app should be available at localhost:3000

Mongo

WRITE_DATA_HERE=...
mongod --dbpath=${WRITE_DATA_HERE}

Backend

1. Update lims_user_config_prod with what is available on dev/prod. We need the values for username, password, & secret_key. Note - This is copied into lims_user_config on make run-prod. On the host, see /srv/www/new-igo-qc/app/lims_user_config.

   scp igo.mskcc.org:/srv/www/new-igo-qc/app/lims_user_config lims_user_config_prod

2. Install virtual environment

   Python 2

   # pip install virtualenv    # If not already installed
   $ virtualenv venv

   Python 3

   # pip3 install virtualenv   # If not already installed
   python3 -m venv venv

3. Install Dependencies

   $ source venv/bin/activate
   (venv) $ pip install -r requirements.txt
   (venv) $ make run

   Note - make run-prod is a Makefile command. If there are issues w/ this step, please review the run-prod step of the Makefile

Frontend

cd static/seq-qc/
npm install && npm run start

Troubleshooting

Mongo

• Is mongo running? i.e. The mongo command allows you to connect to your mongo instance. If mongo is running, you should see something like below -

  $ ps -ef | grep mongo
  1774903000 39995 39879   0 12:40PM ttys001    0:00.75 /Users/streidd/data/mongodb-macos-x86_64-4.2.1/bin/mongod --dbpath=/Users/streidd/data/db

• Do you have write access to the directory specified in --dbpath=?

  $ ls -ltr /Users/streidd/data | grep db
  drwxr-xr-x     73 streidd  MSKCC\Domain Users      2336 Oct 25 12:40 db

Deployment Steps

HOST=igo.mskcc.org  # Production
# HOST=dlviigoweb1  # Development
make HOST=${HOST} deploy

Notes:

• This DELETES the existing application on the HOST specified. It then copies the packaged application created locally to the new location.
• This creates and copies a dist directory to the deployments directory in your home on the HOST specified. Make sure your ~/deployments exists on that HOST!
• make deploy is a Makefile command. If there are issues w/ this step, please review the deploy step of the Makefile
• Expect to enter your password four times - once to scp the packaged application, once to remotely send the install command, and twice to run dzdo remotely (dzdo allows for root access on our VM's and is needed so you can re-deploy if another user was the last to deploy)