From 569329fd3d391a7e63413ac5ae015705b3452af6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Wed, 20 Sep 2023 14:30:16 +0200 Subject: [PATCH] [DOC] simplifying the install doc --- INSTALL.md | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/INSTALL.md b/INSTALL.md index 3523f483..f7a17eb3 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -6,17 +6,19 @@ ## 2 - Clone the code -First, install [Datalad](https://www.datalad.org/). This will allow you to get the code as well as "links" to the data, because the NARPS data is bundled in this repository as [datalad subdatasets](http://handbook.datalad.org/en/latest/basics/101-106-nesting.html). +First, install [Datalad](https://www.datalad.org/). This will allow you to access the NARPS data easily, as it is included in the repository as [datalad subdatasets](http://handbook.datalad.org/en/latest/basics/101-106-nesting.html). Then, [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the project : ```bash +# Replace YOUR_GITHUB_USERNAME in the following command. datalad install --recursive https://github.com/YOUR_GITHUB_USERNAME/narps_open_pipelines.git ``` > [!WARNING] -> It is still possible to clone the fork using [git](https://git-scm.com/) ; but doing this, you will only get the code, loosing the links to the data. +> It is still possible to clone the fork using [git](https://git-scm.com/) ; but by doing this, you will only get the code. > ```bash +> # Replace YOUR_GITHUB_USERNAME in the following command. > git clone https://github.com/YOUR_GITHUB_USERNAME/narps_open_pipelines.git > ``` @@ -38,9 +40,9 @@ datalad get data/original/ds001734/derivatives/fmriprep/sub-00[1-4] -J 12 ## 4 - Set up the environment -The Narps Open Pipelines project is build upon several dependencies, such as [Nipype](https://nipype.readthedocs.io/en/latest/) but also the original software packages used by the pipelines (SPM, FSL, AFNI...). +The Narps Open Pipelines project is build upon several dependencies, such as [Nipype](https://nipype.readthedocs.io/en/latest/) but also the original software packages used by the pipelines (SPM, FSL, AFNI...). Therefore, we created a Docker container based on [Neurodocker](https://github.com/ReproNim/neurodocker) that contains software dependencies. -Therefore, we created a Docker container based on [Neurodocker](https://github.com/ReproNim/neurodocker) that contains the necessary Python packages and software. [Install Docker](https://docs.docker.com/engine/install/) then pull the Docker image : +[Install Docker](https://docs.docker.com/engine/install/) then pull the Docker image : ```bash docker pull elodiegermani/open_pipeline:latest @@ -50,26 +52,28 @@ Once it's done you can check the image is available on your system : ```bash docker images + REPOSITORY TAG IMAGE ID CREATED SIZE docker.io/elodiegermani/open_pipeline latest 0f3c74d28406 9 months ago 22.7 GB ``` > [!NOTE] -> Feel free to read this documentation page [docs/environment.md](docs/environment.md) to start the environment from it. +> Feel free to read this documentation page [docs/environment.md](docs/environment.md) to get further information about this environment. ## 5 - Run the project Start a Docker container from the Docker image : ```bash -docker run -it -v :/home/neuro/code/ elodiegermani/open_pipeline +# Replace PATH_TO_THE_REPOSITORY in the following command (e.g.: with /home/user/dev/narps_open_pipelines/) +docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ elodiegermani/open_pipeline ``` -Install NARPS Open Pipeline inside the container : +Install NARPS Open Pipelines inside the container : ```bash source activate neuro cd /home/neuro/code/ -pip insall . +pip install . ``` Finally, you are able to run pipelines : @@ -80,4 +84,4 @@ python narps_open/runner.py ``` > [!NOTE] -> For further information, read [docs/running.md](docs/running.md). +> For further information, read this documentation page [docs/running.md](docs/running.md).