Linux
Install neurocommand on Linux
Requirements:
Required
- python 3.6+ https://docs.conda.io/en/latest/miniconda.html#linux-installers
- singularity https://sylabs.io/guides/3.5/user-guide/quick_start.html
- git
Optional
command line mode (e.g. running on an HPC or CVL)
- Load singularity and for best performance it should be 3.x e.g.
module load singularity/3.5.0
- Load or install aria2 to optimize the download performance of our containers e.g.
module load aria2c
- Run
git clone https://github.com/NeuroDesk/neurocommand.git
to clone the repository - make sure to clone this to a directory with enough storage, write permissions and NOT a symbolic link (to be sure run cd `pwd -P`)! - Run
cd neurocommand
to change into the directory - Run
pip3 install -r neurodesk/requirements.txt --user
to install pre-requisite python packages - Run
bash build.sh --cli
to install in cli mode - Run
bash containers.sh
for installing indiviual containers orbash containers.sh --all
for installing all containers - Run
module use $PWD/local/containers/modules/
to add the containers to your module search path. Add this to your .bashrc if working. - Run
ml avail
to see the installed containers at the top of the list (neurodesk containers will take preference over system modules with the same name). - If a container is not yet there runml --ignore_cache avail
For Lxde desktops
If running on an lxde desktop…
Run bash build.sh --lxde --edit
For Mate desktops
Run bash build.sh --init
(or bash build.sh --lxde --edit
)
lxde/mate: Mate
installdir: Where all the neurocommand files will be stored (Default: ./local)
appmenu: The linux menu xml file. (Usually /etc/xdg/menus/****-applications.menu)
appdir: Location for the .desktop files for this linux desktop (Usually /usr/share/applications)
deskdir: Location for the .directory files for this linux desktop (Typically /usr/share/desktop-directories)
For desktop menus:
sudo bash install.sh
to install
Creates symlinks to menu files in installation dir
sudo bash uninstall.sh
to uninstall
Removes symlinks
To update
Run git pull
Run bash build.sh
install.sh does not need to be run again
To download all containers
Run bash containers.sh --all
Last modified September 30, 2021: cleaned up instructions for CLI (15f018af)