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How to install LIPSIA using Singularity

The easiest way to install Lipsia is via a singularity container. To build a singularity container for lipsia, execute the following command:

> singularity build lipsia.sif ./singularity-recipe.txt

This creates a container called "lipsia.sif". Its size is around 220 MByte. To execute programs within this container, do the following:

> ./lipsia.sif exec vsml

This will execute the lipsia-program called "vsml". Other lipsia-programs can be called in a similar way.

Install LIPSIA from source (Linux/Unix/MacOS) ========================================

1) Install the necessary compilers and libraries

  • gcc, g++
  • gsl dev
  • boost dev
  • zlib dev
  • python: numpy, matplotlib
  • git

Ubuntu:

sudo apt-get install build-essential libgsl0-dev libboost-dev zlib1g-dev python-tk git-core
sudo pip install numpy matplotlib

Fedora:

sudo dnf install g++ gcc git zlib-devel boost-devel gsl-devel zlib-devel
sudo pip install numpy matplotlib

( "yum" instead of "dnf" for Red Hat, Centos, and the like )

MacOS:

You will need to install

  • command-line-tools
  • homebrew
  • gcc
  • gsl
  • boost
To install these, open a terminal (Applications/Utilities/Terminal). Then run the following commands:
xcode-select --install
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install gcc
brew install gsl
brew install boost
2) Clone the git repository:
git clone https://github.com/lipsia-fmri/lipsia.git

3) Execute the script "lipsia-setup.sh" (in a shell)

cd <lipsia_dir>
source ./lipsia-setup.sh

4) Compile lipsia

cd <lipsia_dir>/src
make

where <lipsia_dir> is the directory of the lipsia repository. All executables can be found in <lipsia_dir>/bin.

5) Change bash profile

:

The following changes need to be performed to your local bash profile (for ubuntu ~/.bashrc, for OSX ~/.bash_profile) Furthermore, the library path needs to be set. Add the following two lines to

PATH=<lipsia_dir>/bin:$PATH
export LD_LIBRARY_PATH=<lipsa_dir>/lib:$LD_LIBRARY_PATH

Install LIPSIA using Docker

1) Install docker on your local machine

Please follow the instructions: https://docs.docker.com/install/

2) Clone the git repository:
git clone https://github.com/lipsia-fmri/lipsia.git

3) Build the Dockerfile

::

cd <lipsia_dir> docker build -t lipsia .

After the installation, you can run any lipsia program by prepending docker run lipsia, e.g.

docker run -v ${dir}:${dir} lipsia vecm -in ${dir}/fmri.v -mask ${dir}/mask.v -out ${dir}/ecm.v

where $dir is the path to the local directory containing your data file, e.g. ${dir}/fmri.v must exist as a file on your local system.