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update python setup and remove neurodocker setup for manual container…
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iishiishii committed Jun 8, 2024
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Expand Up @@ -14,36 +14,12 @@ Refer to [neurodocker](https://github.com/NeuroDesk/neurodocker) for more inform
### Environment Requirements
- Linux environment where you have admin privileges (i.e., can run 'sudo')
- Docker
- Recent Python3 Version
Search for "python_requires" in https://github.com/NeuroDesk/neurodocker/blob/master/setup.cfg for minimal version of Python3 required.
- If you also have Python2 installed, follow these instructions to ensure the 'python' command launches python3: https://stackoverflow.com/questions/68792446/how-to-set-python3-as-default
- Python `>=3.8`. If you have lower Python version, create a virtual environment `conda create -n neurodocker python=3.8 -y` and activate it `conda activate neurodocker`.
- If you have several versions of Python3 installed in the environment, typing 'python' in the terminal should launch a version with equal or higher version number
- Python pip3
This should be launched by 'python -m pip'
- git

### Install Neurodocker
Neurodocker is the dependency we use to build containers.
1. (optional) Sync upstream repository:
If you have the permissions to do so: Press "Fetch upstream" in https://github.com/NeuroDesk/neurodocker to check if our fork of Neurodocker is already up-to-date. Otherwise, open an issue in https://github.com/NeuroDesk/neurocontainers/issues, requesting to pull-in latest changes from Neurodocker upstream into our fork of Neurodocker. One of the admins will attend the issue and perform the operation.
2. (optional) Add a new neurodocker tool:
If relevant to your project, add an option to neurodocker that installs new software (https://github.com/NeuroDesk/neurodocker) and create a pull request to neurodocker's main repository (add new tool in a branch!).
3. Clone our fork of Neurodocker:
```bash
git clone https://github.com/NeuroDesk/neurodocker/
```
4. Install neurodocker:
```bash
cd neurodocker
python -m pip install .
cd ..
```
5. Append line to .bashrc for adding the path:
```bash
echo 'export PATH=${PATH}:${HOME}/.local/bin' >> ${HOME}/.bashrc
```
6. Close the terminal, and reopen it for the updated PATH to take effect


### Fork the Neurocontainers repository
- Fork neurocontainers and setup github actions.
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