scDB 0.0.1

single cell database utilities

Update Data Model

EGA

1. Write a function (named by the EGAID) to preprocess meta table under the EGA class in scDB/EGA.py file
2. Enter the following CMD to update data mode

./bin/scDB [project] [workspace] EGA [path/to/delimited_maps] [EGAID]

CCG

Process previous project

1. Write a function (named by the cohortID) to preprocess meta table under the CCG class in scDB/CCF.py file
2. Enter the following CMD to update data mode

./bin/scDB [project] [workspace] CCG [path/to/meta_table] [cohortID]

Update BCL file to the shared workspace [SingleCellStorage_VALab]

1. Copy the BCL file to gs://fc-48fd2ee8-f6eb-4d07-b271-e8304d29fb1b/Raw_BCL_Files
2. Copy Manifest file to gs://fc-48fd2ee8-f6eb-4d07-b271-e8304d29fb1b/Manifest_Files/[cohort_id]_Manifest.txt
3. Manually generate a [cohort_id].tsv file
4. Enter the following CMD to update data mode

./bin/scDB nci-breardon-bi-org SingleCellStorage_VALab CCG meta/CCG/BCL/[cohort_id].tsv bclStorage