MiModD Installation Examples

The simple case - all required software pre-installed

# system-wide installation
# requiring admin rights

sudo python3 -m pip install MiModD -v

Installation for just the current user

# no admin rights required

python3 -m pip install MiModD --user -v

Installation into virtual environment

Requirement

Python 3.4+

# create virtualenv named wgs
# assuming there is no pip installed with system python3

python3 -m venv ~/wgs --without-pip

# activate the virtualenv
# will need to do this at the beginning of every new session

. ~/wgs/bin/activate

# get pip into virtualenv and install MiModD

wget https://bootstrap.pypa.io/get-pip.py
python3 get-pip.py
python3 -m pip install MiModD -v

# remove ambiguous python link if you are using MiModD from Galaxy;
# you definitely want to avoid Galaxy mistaking this for Python2

rm ~/wgs/bin/python

# end the virtualenv session
deactivate

Installation into user-defined directory

Note

This is the closest to a portable install of MiModD, but is currently not well tested. An installation into a virtual environment is probably almost always preferable.

python3 -m pip install MiModD --target ~/myMiModD

# using this installation is only possible from within the specified folder

cd ~/myMiModD

# make the mimodd executable easier to reach

ln MiModD/bin/mimodd mimodd

# configure the package and start using it

python3 -m MiModD.config
./mimodd help

Installation for the current user without pip on OS X

# assuming the MiModD-0.1.7.3 wheel file for Python 3.5 has been downloaded
# from https://sourceforge.net/projects/mimodd/files
# and renamed (for readability of the example) MiModD-0.1.7.3-cp35.whl

python3 ~/Downloads/MiModD-0.1.7.3-cp35.whl --user

Installation for the current user without pip on Linux

# assuming the self-installing source zip file for MiModD-0.1.7.3 has been
# downloaded from https://sourceforge.net/projects/mimodd/files

python3 ~/Downloads/MiModD-0.1.7.3-source-install.zip --user

Installation from scratch on a VERY naive Ubuntu system

sudo apt-get install zlib1g-dev
sudo apt-get install g++ python3-dev make
wget https://bootstrap.pypa.io/get-pip.py
sudo python3 get-pip.py
sudo python3 -m pip install MiModD -v

Installation on a fresh Fedora 23 system

sudo dnf install zlib-devel
sudo dnf install python3-devel
sudo dnf install gcc
sudo dnf install gcc-c++
sudo dnf install redhat-rpm-config
python3 -m pip install MiModD --user -v