BioNexus
Setting up database
-
Copy
.env.example->.envand adjust -
Start Postgres + Adminer:
docker-compose up -d db adminer
Adminer available at http://localhost:8080 (server: db, user: bionexus, db: bionexus)
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(Optional) Create local env using
conda:conda create -n bionexus python=3.10 conda activate bionexus pip install -e .[dev]
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Create/upgrade schema:
bionexus upgrade head
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Load data:
RetroMol and BioCracker results can be loaded with the load command. For more information, run:
bionexus load --help
Examples of scripts that extract annotations and references from RetroMol and BioCracker can be found in the
scripts/folder. -
Dump for deployoment:
Make sure the database is running in Docker, then:
bionexus dump --out ~/Downloads/dumps/bionexus_$(date +%Y%m%d).dump
1 maintainer
Metadata
1 maintainer
Release files for bionexus 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| bionexus-0.1.0.tar.gz | 21.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bionexus-0.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 36.5 kB
Release files / bionexus-0.1.0.tar.gz
| Download URL | bionexus-0.1.0.tar.gz |
|---|---|
| Size | 21.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.10.19
|
Release files / bionexus-0.1.0-py3-none-any.whl
| Download URL | bionexus-0.1.0-py3-none-any.whl |
|---|---|
| Size | 14.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.10.19
|
