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Updating README
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Signed-off-by: Sebastian <sebastian.franz@tum.de>
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SebieF committed Sep 10, 2024
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Expand Up @@ -12,22 +12,25 @@ These are the currently provided modules:
| embeddings | Embed protein sequences | [biotrainer] |
| ppi | Work with protein-protein interactions | [hvi_toolkit] |
| prediction_models | Train and evaluate models trained on embeddings | [biotrainer] |
| proteins | Work with protein data | [hvi_toolkit] |
| proteins | Work with protein data | [taxoniq] |

[biotrainer]: https://github.com/sacdallago/biotrainer

[hvi_toolkit]: https://github.com/SebieF/hvi_toolkit

[taxoniq]: https://github.com/taxoniq/taxoniq

## Supported platforms

`Biocentral` and `biocentral_server` are designed to provide all common desktop operating systems
(Windows, Linux, macOS).
`Biocentral` and `biocentral_server` are designed to provide all common desktop operating systems
(Windows, Linux, macOS).
The following table gives an overview about the current test and packaging status:

| OS | Tested | Packaging |
|--------------|:-------:|:---------:|
| Ubuntu 24.04 || .zip |
| Ubuntu 22.04 || .zip |
| Windows 10 | planned | tbd |
| Windows 10 | | .zip |
| Windows 11 | planned | tbd |
| macOS | planned | tbd |

Expand Down Expand Up @@ -56,26 +59,45 @@ poetry run run-biocentral_server.py --headless

## Building

Building and bundling is done using [pyinstaller](https://pyinstaller.org/en/stable/) and `make`.
Building and bundling is done using [pyinstaller](https://pyinstaller.org/en/stable/) and `make`.

On Windows, you can use `winget` to install `make`:

```shell
winget install ezwinports.make
```

Check that all build variables are correct:

```shell
make print-info
```

Then call build:

```shell
make build
```

To create a `zip` file with all required files for distribution:

```shell
make bundle
```

*Note that this file only works on the operating system version you ran `make build` on!*


# Citation

Please cite the [biocentral main repository](https://github.com/biocentral/biocentral) if you are using
biocentral_server in your scientific publication:

```text
@Online{biocentral,
accessed = {2024-09-10},
author = {Biocentral contributors},
title = {Biocentral - An open source bioinformatics application},
url = {https://github.com/biocentral/biocentral},
}
```

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