https://github.com/pepkit/pephubclient
A tool to provide Python and CLI interface and Python API for PEPhub.
https://github.com/pepkit/pephubclient
bioinformatics command-line-tool project python
Last synced: 3 months ago
JSON representation
A tool to provide Python and CLI interface and Python API for PEPhub.
- Host: GitHub
- URL: https://github.com/pepkit/pephubclient
- Owner: pepkit
- License: bsd-2-clause
- Created: 2022-07-08T17:16:40.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2026-03-18T18:47:09.000Z (3 months ago)
- Last Synced: 2026-03-28T00:42:39.796Z (3 months ago)
- Topics: bioinformatics, command-line-tool, project, python
- Language: Python
- Homepage: https://pephub.databio.org
- Size: 345 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
PEPHubClient
[](https://pepkit.github.io)
[](https://pypi.org/project/pephubclient)
[](https://pypi.org/project/pephubclient)
[](https://coverage-badge.samuelcolvin.workers.dev/redirect/pepkit/pephubclient)
[](https://github.com/pepkit/pephubclient)
[](https://github.com/psf/black)
`PEPHubClient` is a tool to provide Python API and CLI for [PEPhub](https://pephub.databio.org).
---
**Documentation**: https://pep.databio.org
**Source Code**: https://github.com/pepkit/pephubclient
---
## Installation
To install `pepdbagent` use this command:
```
pip install pephubclient
```
or install the latest version from the GitHub repository:
```
pip install git+https://github.com/pepkit/pephubclient.git
```
---
### `pephubclient` features:
1) `push` (upload) projects)
2) `pull` (download projects)
Additionally, our client supports pephub authorization.
The authorization process is based on pephub device authorization protocol.
To upload projects or to download private projects, user must be authorized through pephub.
If you want to use your own pephub instance, you can specify it by setting `PEPHUB_BASE_URL` environment variable.
e.g. `export PEPHUB_BASE_URL=https://pephub.databio.org/` (This is original pephub instance)
To login, use the `login` argument; to logout, use `logout`.
----
```text
$ phc --help
Usage: pephubclient [OPTIONS] COMMAND [ARGS]...
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --version -v │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the │
│ installation. │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ login Login to PEPhub │
│ logout Logout │
│ pull Download and save project locally. │
│ push Upload/update project in PEPhub │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
```
```text
$ phc pull --help
Usage: pephubclient pull [OPTIONS] PROJECT_REGISTRY_PATH
Download and save project locally.
╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * project_registry_path TEXT [default: None] [required] │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --force --no-force Overwrite project if it exists. [default: no-force] │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
```
```text
$ phc push --help
Usage: pephubclient push [OPTIONS] CFG
Upload/update project in PEPhub
╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * cfg TEXT Project config file (YAML) or sample table (CSV/TSV)with one row per sample to constitute │
│ project │
│ [default: None] │
│ [required] │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * --namespace TEXT Project namespace [default: None] [required] │
│ * --name TEXT Project name [default: None] [required] │
│ --tag TEXT Project tag [default: None] │
│ --force --no-force Force push to the database. Use it to update, or upload project. │
│ [default: no-force] │
│ --is-private --no-is-private Upload project as private. [default: no-is-private] │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
```