A progressive Node.js framework for building efficient and scalable server-side applications.

Description

Nest framework TypeScript starter repository.

Installation

$ npm install

Running the app

# development
$ npm run start

# watch mode
$ npm run start:dev

# production mode
$ npm run start:prod

Test

# unit tests
$ npm run test

# e2e tests
$ npm run test:e2e

# test coverage
$ npm run test:cov

Support

Nest is an MIT-licensed open source project. It can grow thanks to the sponsors and support by the amazing backers. If you'd like to join them, please read more here.

Stay in touch

• Author - Kamil Myśliwiec
• Website - https://nestjs.com
• Twitter - @nestframework

License

Nest is MIT licensed.

Deploy local version

Client and server

Download and init CSTB client and server

git clone https://github.com/MMSB-MOBI/cstb2-server
cd cstb2-server
npm i
cd ..
git clone https://github.com/MMSB-MOBI/cstb-client
npm i

Job manager

Clone and init ms-jobmanager

git clone https://github.com/MMSB-MOBI/ms-jobmanager.git
cd ms-jobmanager
npm i

Launch ms-jobmanager for local computation

node bin/startServer.js -e emulate -p 6000 -k 6001 -c <cache directory> --force

Change adress and listening port in config_local.yaml

job-manager:
  address: "localhost"
  port: 6001

Motif-broker

Clone and init motif-broker

git clone https://github.com/MMSB-MOBI/motif-broker
cd motif-broker
npm i

You need to have a local version of couch database (How to construct it ? https://github.com/MMSB-MOBI/CSTB_database_manager) or redirect the server version :

# Redirect arwen-cdb.ibcp.fr:5984 to localhost:1234
ssh arwen -L 1234:arwen-cdb.ibcp.fr:5984

Launch motif-broker

node build/index.js -f prefix_rules.json -d http://<user>:<password>@localhost -p 1234 -l 6003

Update config_local.yaml

db:
  couchDB:
    connect:
      user: <user>
      password: <password>
      host: 'localhost'
      port: 1234
  
  motif-broker:
    host: 'localhost'
    port: 6003

Environments and tools

crispr-set

Install crispr-set

git clone https://github.com/glaunay/crispr-set
python setup.py build
ln -s build/lib.linux-x86_64-3.7/*so twobits.so
gcc -Wall -std=c99 main.c custom_*.c two_bits_encoding.c -I./include -o setCompare -pedantic -lm

Change $PATH variable to include setCompare binary in crispr_workflow_local.sh and crispr_workflow_specific_local.sh

export PATH=$PATH:<crispr-set path>

CSTB scripts

Create python3 venv to install pip dependencies

python -m venv cstb_env
source cstb/bin/activate
cd cstb_env
git clone https://github.com/MMSB-MOBI/CSTB
cd CSTB
pip install -r requirements.txt

Load env and include CSTB module in PYTHONPATH in crispr_workflow_local.sh and crispr_workflow_specific_local.sh

source <csbt_env_path>/bin/activate
CRISPR_TOOLS_SCRIPT_PATH=<csbt_env_path>/CSTB/bin
export PYTHONPATH=<csbt_env_path>/CSTB/lib

Blast

Blast is only used for specific gene part.

If you already have blast installed or if you want a global version you can install it on your computer and be sure the binaries are in your PATH or include them through export PATH in crispr_workflow_specific_local.sh

As an alternative you can also create a conda environment and install blast inside it :

conda create -n blast
conda activate blast
conda install -c bioconda blast

Then load env in crispr_workflow_specific_local.sh :

source <miniconda/anaconda path>/etc/profile.d/conda.sh #needed to call conda activate inside bash script
conda activate blast

You may need to change other parameters such as filesystem database in config_local.yaml

Start the dev server

Be sure config_local.yaml is load in src/config/configuration.ts

const YAML_CONFIG_FILENAME = 'config_local.yaml';

Launch server in watch mode:

cd <cstb2-server path>
npm run start:dev

Launch client

cd <cstb-client path>
npm run serve