Linux

Ways of using Neurocommand in Linux:

1. You can use the module files for Neurocontainers directly via CVMFS: https://www.neurodesk.org/docs/getting-started/neurocontainers/cvmfs/
2. or you can install Neurocommand as described here:

Requirements:

Required

• python 3.6+ https://docs.conda.io/en/latest/miniconda.html#linux-installers
• singularity https://docs.sylabs.io/guides/3.5/user-guide/quick_start.html
• git
• lmod https://lmod.readthedocs.io/en/latest/

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 individual containers or bash 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. When adding to your .bashrc you will need to replace $PWD to point to the correct path, i.e. module use ~/neurocommand/local/containers/modules/.
• 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 run ml --ignore_cache avail
• Every time you start a new shell you need to run module use PathToYourContainers or add this command to you .bashrc file.

GPU support

Some of our containers contain GPU-accelerated applications. Here is an example that runs the GPU accelerated program eddy in FSL:

module load fsl/6.0.5.1
export neurodesk_singularity_opts='--nv'
eddy_cuda9.1

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

For user-specific desktop menus in a shared Linux environment

mkdir -p $HOME/.config/menus
mkdir -p $HOME/.local/share/applications
mkdir -p $HOME/.local/share/desktop-directories
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/xfce-applications.menu $HOME/.config/menus
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/neurodesk-applications.menu $HOME/.config/menus
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/applications $HOME/.local/share/applications/neurodesk
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/desktop-directories $HOME/.local/share/desktop-directories/neurodesk

To update

Run git pull
Run bash build.sh # this updates the neurocommand but not the modules install.sh does not need to be run again to update containers go into the neurodesktop directory and run bash containers.sh Choose the module you want to update for example you want to update mrtrix3/3.0.2 module with the eddy_cuda fix: ~/neurocommand/local/fetch_containers.sh mrtrix3 3.0.2 20221108 mrview $@

To download all containers

Run bash containers.sh --all