Installation

Requirements

To run pysmFISH you will need python >=3.6 (we have no plans to support python<3.6). The code has still some dependencies from MPI (we are currently removing them). Install mpich2 on linux using

apt-get install -y mpich

or on OSX using

brew install mpich2

Install using PyPI

Every new stable version of pysmFISH gets immediately released on PyPI, so running the following command will install on your system the cutting-edge version:

pip install --no-cache-dir pysmFISH

To get started with pysmFISH you can follow our guide.

Install from source

If you plan to explore and make changes to the source code, or you have requested some bug-fix that is temporarily available only on the github dev branch, then you need to install pysmFISH directly from source.

First of all, make sure all the dependencies are installed, and that git is installed on your system. Then, run the following commands to complete the installation:

git clone https://github.com/linnarsson-lab/pysmFISH.git
cd pysmFISH.py
pip install -e .  # note the trailing dot

You can test whether the installation was successful by running pysmFISH --help.

Tip

pysmFISH is an alpha release, we recommend pulling in the latest bufixes and feature improvements often. Note that adding the -e flag to the pip command installs the software in development mode, when a package is installed this way each change to the source immediatelly reflects to changes in the installed library. This means that you can simply use git pull to update your installation.

To get started with pysmFISH you can follow our guide.

Install using conda

Note

This installation method is not currently available. Our plan is make it available asap.