Installation

Set up a virtual environment

To ensure that Merlin and its dependencies don’t interfere with other packages that are installed, we recommend that you install MERlin in a new virtual environment. MERlin requires python 3.6 or above.

An anaconda virtual environment can be created using the command:

conda create -n merlin_env python=3.6

and the new environment can be activated using the command:

conda activate merlin_env

or

source activate merlin_env

Installing prerequisites

The packages rtree and pytables are not properly installed by pip and should be installed independently. For example, using Anaconda:

conda install rtree pytables

On Harvard research computing, matplotlib raises an error saying that ‘CXXABI_1.3.9’ is not found. This can be corrected by loading the gcc module:

module load gcc/8.2.0-fasrc01

Installing MERlin

MERlin can be installed by cloning the repository and installing with pip:

git clone https://github.com/emanuega/MERlin

pip install -e MERlin

Specifying paths with a .env file

A .env file is required to specify the search locations for the various input and output files. The following variables should be defined in a file named .env in the user home directory (~.env on linux or C:usersUserName.env on Windows):

  • DATA_HOME - The path of the root directory to the raw data.

  • ANALYSIS_HOME - The path of the root directory where analysis results should be stored.

  • PARAMETERS_HOME - The path to the directory where the merfish-parameters directory resides.

The PARAMETERS_HOME directory should contain the following folders: * analysis - Contains the analysis parameters json files. * codebooks - Contains the codebook csv files. * dataorganization - Contains the data organization csv files. * positions - Contains the position csv files. * microscope - Contains the microscope parameters json files. * fpkm - Contains the fpkm csv files. * snakemake - Contains the snakemake arguments json files.

An example PARAMETERS_HOME directory with typical files can be found in the merlin-parameters-example repository.

The contents of an example .env file are below:

DATA_HOME=D:/data
ANALYSIS_HOME=D:/analysis
PARAMETERS_HOME=D:/merfish-parameters