ProteoMutics (In-Development)

a bioinformatics program that plots patterns between mutations and nucleosomes

START FRONTEND

cd ./frontend
npm install
npm run start

INSTALL AND START BACKEND WITHOUT DOCKER

cd ./backend
pip install -r requirements.txt
uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload --reload-include "*"

START BACKEND

cd ./backend
uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload --reload-include "*"

CREATE AND START DOCKER ENVIRONMENT (DEVELOPMENT)

docker-compose up -d --build

START DOCKER ENVIRONMENT (DEVELOPMENT)

docker-compose up -d proteomutics-api

EXECUTE COMMANDS IN DOCKER ENVIRONMENT (DEVELOPMENT)

docker-compose exec app bash

CREATE AND START BACKEND WITH DOCKER (PRODUCTION)

docker build -t proteomutics-api .
docker run -d -p 8000:8000 proteomutics-api

/home/cam/Documents/repos/ProteoMutics/backend/test/test_data/UV.vcf /home/cam/Documents/repos/ProteoMutics/backend/test/test_data/dyads.bed /home/cam/Documents/repos/ProteoMutics/backend/test/test_data/hg19.fa /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/nucleosome/hg19_MNase_nucleosome_map_all.bed /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/lesion_files/proteomutics/vcf/SRR_64-65-66_subset.vcf /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/lesion_files/proteomutics/vcf/SRR_64-65-66.vcf /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/lesion_files/proteomutics/vcf/SRR_67-68.vcf /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/lesion_files/proteomutics/vcf/SRR_69-70.vcf /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/vcf_files/genotype_split/HMCES_KBr.vcf /media/cam/Working/8-oxodG/8-oxodG_Final_Analysis/vcf_files/genotype_split/WT_KBr.vcf