Standard Installation

Instructions for OS X / macOS (10.9 - 10.15)

Requirements

  • Python 3.3+
  • optional: the pip installation tool for one-step installation

  1. Install Python 3

    Download the latest release of Python 3 from https://www.python.org/downloads/ and run the installer. Make sure you choose to install pip if the install wizard offers you to do so.

Warning

The current version of MiModD is incompatible with Python versions >= 3.7.5. The next release of MiModD will address this issue, but until then make sure you use Python 3.6 or earlier.

  1. Install MiModD

    1. with pip installed along with Python 3

      Open a terminal window and run:

      python3 -m pip install MiModD --user

      to install the latest version of MiModD for the current user.

      If you prefer [1] a system-wide install visible for all users run:

      sudo python3 -m pip install MiModD

      and authenticate yourself as administrator when prompted to do so.

    Alternatively (if you chose to or for some reason are not able to use pip):

    1. without pip

      • Visit https://sourceforge.net/projects/mimodd/files and navigate to the latest release folder.

      • Download the …-cp##-cp##m-macosx… whl file for which ## matches the Python version you installed in step 1.

      • Open a terminal window and run:

        python3 <download_folder>/<whl_file_name> --user

        to install MiModD for the current user [1], or:

        sudo python3 <download_folder>/<whl_file_name>

        for a system-wide install.

    See also

    MiModD Installation Examples for a compilation of real-world and tested ways to install MiModD from the command line

  2. Start using MiModD!

Instructions for Linux and other platforms

Requirements

  • a C/C++ compiler (tested with gcc/g++ and Clang)
  • the make utility
  • zlib library version 1.2.5+ including the developer header files
  • Python 3.3+ including the developer header files
  • optional: the pip installation tool for Python for one-step installation

  1. Install requirements

    Different Linux distributions come with different subsets of the above requirements preinstalled and may offer others through their package management system. Please read Installation of required software for more details.

Warning

The current version of MiModD is incompatible with Python versions >= 3.7.5. The next release of MiModD will address this issue, but until then make sure you use Python 3.6 or earlier.

  1. Install MiModD (this may take a few minutes)

    1. with pip installed for Python 3

      Open a terminal window and run:

      python3 -m pip install MiModD --user

      to install the latest version of MiModD for the current user.

      If you prefer [1] a system-wide install visible for all users run:

      sudo python3 -m pip install MiModD

      and authenticate yourself as administrator when prompted to do so.

    Alternatively (if you chose to or for some reason are not able to use pip):

    1. without pip

      • Visit https://sourceforge.net/projects/mimodd/files and download the self-installing zip file found in the latest release folder.

      • Open a terminal window and run:

        python3 <download_folder>/<zip_file_name> --user

        to install MiModD for the current user [1], or:

        sudo python3 <download_folder>/<zip_file_name>

        for a system-wide install.

    See also

    MiModD Installation Examples for a compilation of real-world and tested ways to install MiModD (and some typical required packages) from the command line

  2. Start using MiModD!

[1](1, 2, 3, 4) On OS X and some Linux distributions an inconvenience of installing MiModD for only the current user is that the mimodd executable will not be found automatically by the system. This can be fixed by manually adding the mimodd executable to the $PATH environment variable.

Start using MiModD

The first thing you should do after having installed MiModD successfully is to configure the package.

For a fresh install, running:

python3 -m MiModD.config

will invoke a simple configuration wizard that will help you choose the right settings for your system in a few steps.

Note

The wizard will require write access to the package files you just installed. If you used sudo to install MiModD with administrator privileges, you will have to prepend it to the above line as well (and will have to do so everytime you want to change configuration settings).

Once configuration is done, try executing:

mimodd help

This should display an overview of available tools and help topics.

You can use mimodd help <tool name> to get more detailed help on a specific tool, e.g.:

mimodd help annotate

Note

If, instead of the expected help output, you are getting a command not found or a similar error message, you should read our recipe for adding the mimodd executable to the $PATH environment variable.

See also

Adding additional functionality

MiModD is designed to provide all essential functionality for a complete mapping-by-sequencing analysis workflow out of the box. Though lightweight the package lets you align NGS reads to a reference genome, determine sequence variants based on the alignment, filter the variants and perform different types of variant linkage analysis to pinpoint variants causing selected phenotypes. That said, the core functionality provided by the package can be extended through the installation of additional third party tools and libraries. Specifically, you can install

  • the variant annotation software SnpEff, which will enable MiModD to create significantly easier to interpret variant reports that include the functional effects of variants on genes and gene products and/or
  • the combination of R and rpy that MiModD can use to produce publication-quality variant linkage plots right on your local machine

See also

In addition, you can set up your own local Galaxy server and integrate MiModD into it. With Galaxy you will enjoy:

  • a graphical user interface for composing and managing your analyses
  • a simple interface for rerunning previous analyses steps and for executing several steps in parallel
  • server functionality that lets you access MiModD through the browser of any computer in your network

See also

The chapter Galaxy Installation and Initial Configuration has step-by-step instructions for getting Galaxy running and for integrating your existing installation of MiModD into it.

Note

As one restriction compared to a toolshed installation of MiModD, you cannot currently have multiple versions of standard installations accessible from within the same instance of Galaxy. When you upgrade a standard installation, this will include a Galaxy tool wrapper upgrade, but there is no way to do this and keep the old version available at the same time.

Keeping MiModD updated

We are always trying to improve MiModD and release new package versions with enhancements and bug-fixes regularly.

In order to keep you informed about available new versions and to facilitate upgrades, MiModD features a dedicated upgrade tool.

You can run, at any time:

python3 -m MiModD.upgrade

to check if there is a new version of MiModD available.

If a new version is found, you can run (possibly with a prepended sudo):

python3 -m MiModD.upgrade install

to upgrade to the latest version.

Warning

Due to changes in the tool, upgrades from versions prior to v0.1.7 need to be done sequentially by first upgrading to v0.1.7.0, then to the latest version. This can be done by running:

python3 -m MiModD.upgrade install -v 0.1.7.0

before the standard upgrade command above.

In addition, upgrades from versions prior to v0.1.8 will require enabling MiModD for Galaxy again even if the old version had been used through Galaxy already.

See also

The upgrade tool for a complete description of all available options