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Installation
Liu Mengxing edited this page Nov 23, 2022
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There are four ways to run (and hence install) anatROIs:
- Install a docker client in your machine, see Docker installation.
- Launch the command:
docker pull garikoitz/anatrois:<version> - We tested in Linux and MacOS
Follow this instructions for converting Dockers to singularity. Our containers have been tested in Singularity, usually no further adjustments are required, but it can depend on Singularity installation specifics.
What we usually do to create singularity images is:
- Login to the HPC Cluster
- module load singularity
$ mkdir path/to/where/you/want/to/store/your_singularity_images$ cd path/to/where/you/want/to/store/your_singularity_images$ singularity build ./anatROIs_<version>.sif docker://garikoitz/anatROIs:<version>
- Requires a paid Flywheel account, usually provided by your institution.
- If not available in the drop-down analysis gear list, ask your administration to install it.
Everything inside the containers can be run natively. This means that you will need to have all the software that we install in the container installed in your machine. Once you do that, you can:
- Git clone the repositories, prepare the input data and config files and use the
bin/runfile - WE DON'T RECOMMEND THIS PATH. There are other dependencies that we control on the Docker containers that can't be controlled. The libraries will be different, different version in all softwares...
- This should only be used for development and testing purposes. If you want to contribute to the tool by fixing bugs or adding functionalities please let us know and we will help setting it up.