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https://github.com/metgem/metgem
Calculation and visualization of molecular networks based on t-SNE algorithm
https://github.com/metgem/metgem
chemistry chemoinformatics cosine-similarity graph mass-spectrometry metabolomics network networking
Last synced: about 2 months ago
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Calculation and visualization of molecular networks based on t-SNE algorithm
- Host: GitHub
- URL: https://github.com/metgem/metgem
- Owner: metgem
- License: gpl-3.0
- Created: 2018-07-09T15:13:00.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-05-28T15:37:58.000Z (7 months ago)
- Last Synced: 2024-05-29T00:05:34.997Z (7 months ago)
- Topics: chemistry, chemoinformatics, cosine-similarity, graph, mass-spectrometry, metabolomics, network, networking
- Language: Python
- Homepage: https://metgem.github.io
- Size: 18.5 MB
- Stars: 28
- Watchers: 5
- Forks: 3
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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# Download pre-built packages
You can download the latest stable version from [here](https://github.com/metgem/metgem/releases/latest) or latest development version from [here](https://github.com/metgem/metgem/releases/nightly).
# Notes on installation on macOS
Latest versions of MetGem are only compatible with macOS 10.15 Catalina and later.
Currently, MetGem lacks a signature for macOS. As a workaround, user can allow MetGem in the macOS Gatekeeper protection by running the following command in the terminal from the Applications folder.
- Download MetGem and click the .dmg installer - Drag and drop MetGem into the Applications folder.
- Open a Terminal and type the following command to tell macOS to trust the installed version of MetGem:
```
sudo xattr -cr /Applications/MetGem/MetGem.app
```
- Approve command with user password.
- Start MetGem.
- If this fails, try the following command (the app will appear in the security preferences and you will be able to choose the "Open anyway" option):
```
sudo xattr -d com.apple.quarantine /Applications/MetGem/MetGem.app
```
# Installation from source
1. Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
2. Clone the repository:
```
git clone https://github.com/metgem/metgem.git
cd metgem
```
3. Create a new virtual environment
```
conda env create -f environment.yml
conda env update -f environment.dev.yml
```
4. Activate the virtual environment
```
conda activate metgem
```
5. Install build dependencies:
```
conda install invoke
```
6. Build the resource file:
```
invoke rc
```
7. Launch MetGem
```
python MetGem
```
For later use, you just need to activate the environment before launching MetGem