Docent app

Data Prepration

(a) Generate fake affected gene data

Rscript generate_fake_affected_gene_data.r

(b) Export Seruat object to Rds file.

Rscript export_seurat_to_rds.r

(c) Generate genotype.csv file from multisample vcf

Rscript import_vcf_to_genotype_csv.r

(d) Import genotype csv file into sqlite database

Rscript import_genotypes_to_sqlite.sh

Build and push docker image

sh docker_build.sh

Running the app

docker run -p 3838:3838 -v /path to data_folder/pbmc_2018-05-24_dev:/docent_data docker.io/man4ish/docent:latest

path to data folder on gpfs : /home/mkumar1/app_backup/backup_20220708/Docent_app/pbmc_2018-05-24_dev

Example

docker run -p 3838:3838 -v /home/mkumar1/app_backup/backup_20220708/Docent_app/pbmc_2018-05-24_dev:/docent_data docker.io/man4ish/docent:latest

browse the application

http://0.0.0.0:3838