Metadata-Version: 2.1
Name: scDB
Version: 0.0.1
Summary: single cell database utilities
Home-page: https://jingxinfu.github.io/scDB
Author: Jingxin Fu
Author-email: jingxinfu.tj@gmail.com
License: UNKNOWN
Keywords: single cell,terra
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.4, <4
Description-Content-Type: text/markdown
Requires-Dist: firecloud
Requires-Dist: tenacity
Requires-Dist: pandas
Requires-Dist: colorlog

# 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
```



