https://github.com/gyorilab/indra_db_lite

Work with content from indra_db in a local sqlite database.
https://github.com/gyorilab/indra_db_lite

Last synced: 4 months ago
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Work with content from indra_db in a local sqlite database.

• Host: GitHub
• URL: https://github.com/gyorilab/indra_db_lite
• Owner: gyorilab
• License: bsd-2-clause
• Created: 2021-01-13T03:26:37.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2024-10-18T14:39:07.000Z (7 months ago)
• Last Synced: 2024-11-17T12:19:53.164Z (6 months ago)
• Language: Python
• Size: 92.8 KB
• Stars: 0
• Watchers: 2
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# indra_db_lite

Work with content from indra_db in a local sqlite database.

## Installation

Clone this repo and either add the folder into which it was cloned to your

PYTHONPATH, or run `pip install -e .` from within the top level of the folder into

which it was cloned.

If you have a compressed database file stashed

on Amazon S3, set the environment variable `INDRA_DB_LITE_S3_BUCKET` to the S3 bucket

where the database file is located and the environment variable

`INDRA_DB_LITE_LOCATION` to the path where would like the decompressed database file

to be stored on your machine. The database file will be over 150GB when

decompressed so ensure that there is enough space for it. If the S3 key for

the compressed db file is something other than `indra_lite.db.xz`, then set the

environment variable `INDRA_DB_LITE_S3_KEY` to the actual key.

Once these environment variables are set correctly, run

    $ python -m indra_db_lite.download

to download the sqlite db file to your machine and decompress it. Note that it may

take over an hour to download and decompress the db file. Once completed,

indra_db_lite should be ready to use.

## Construction

Run each script in construct/tables separately and then run construct/assembly.