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