Installing on SGE - McIntosh-Lab/tvb-ukbb GitHub Wiki

This page contains instructions for installing the TVB-UKBB pipeline on Sun Grid Engine (SGE) systems (specifically RRI users).

The only external dependencies required for this pipeline are:

• FSL (6.0.4)
• AFNI (18.0.22)
• Freesurfer (5.3.0)
• Anaconda/Miniconda (latest release)
• git (>=2)
• gfortran (installation only)
• OGS/GE (Open Grid Scheduler/Grid Engine version 2011.11)

Note: these software versions are what we used to develop the pipeline. Newer versions may work but we cannot guarantee that.

CONDA SETUP

Note: these instructions are specifically for gateway. This has not been tested on any other system so it is advised to install onto gateway.

• Copy the following and paste it at the bottom of your .bashrc file in your home directory on gateway:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/nfrazier-logue/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/nfrazier-logue/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/nfrazier-logue/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/nfrazier-logue/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

• Create a directory in your home directory called conda_cache.
• Create a file in your home directory on gateway called .condarc and copy the following into it:

channels:
 - defaults
 - anaconda
 - conda-forge
pkgs_dirs:
 - /home/<username>/conda_cache

where <username> on the last line is your gateway username. Continue with the rest of the instructions below.

GENERAL INSTALL INSTRUCTIONS

Clean installation:

1. Download the latest release .zip from the repository here (read the instructions on the release page)
2. Unzip the .zip file to where you'd like the pipeline to be installed; e.g. unzipping it in /home/<username> will yield /home/<username>/tvb-pipeline
3. cd into tvb-pipeline and run chmod +x install_ukbb.sh
4. Run ./install_ukbb.sh. This may take a while and you will have to enter your GitHub username and password midway through as the repository is currently invite-only.
5. Once the installer finishes, cd into tvb-ukbb and edit file init_vars. Lines specified with #TO BE MODIFIED BY USER are the only lines you should need to change.

Reinstallation:

1. Before pulling a new version of the pipeline from github or cloning the repository, install git-lfs (https://git-lfs.github.com) and run git lfs install
2. cd into tvb-pipeline and run chmod +x install_ukbb.sh
3. Run ./reinstall_ukbb.sh.
4. Once the installer finishes, cd into tvb-ukbb and edit file init_vars. Lines specified with #TO BE MODIFIED BY USER are the only lines you should need to change.

Note: at present, changes may need to be made to the code handling Grid Engine/SGE queuing depending on your system. Currently we use queues all.q, bigmem_16.q, and bigmem_64.q; they are set to their respective environment variables by default in init_vars and can be modified as necessary.

We release bugfixes and introduce new features on a rolling basis. If you have been working on a local version or a fork of the pipeline, please be sure to pull the most recent version of the pipeline before you run your data.

Details and instructions for customizing the pipeline to acquisitions can be found in Customizing the Pipeline.