Install

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1) Prerequisite

Before installing orthofisher, please first install HMMER3 and add HMMER to your .bashrc path. For example, my .bashrc has the following:

export PATH=$PATH:/home/steenwj/SOFTWARE/hmmer-3.1b2-linux-intel-x86_64/binaries

2) Install orthofisher

If you are having trouble installing orthofisher, please contact the lead developer, Jacob L. Steenwyk , via email or twitter to get help.

To install via anaconda, execute the follwoing command:

conda install -c jlsteenwyk orthofisher

Visit here for more information: https://anaconda.org/jlsteenwyk/clipkit

To install via pip, execute the follwoing command:

pip install orthofisher

To install from source, execute the follwoing command:

# download
git clone https://github.com/JLSteenwyk/orthofisher.git
# change dir
cd orthofisher/
# install
make install

If you run into software dependency issues, install orthofisher in a virtual environment. To do so, create your virtual environment with the following command:

# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate

Next, install the software using your preferred method above. Thereafter, you will be able to use orthofisher.

To deactivate your virtual environment, use the following command:

# deactivate virtual environment
deactivate

Note, if you install via a virtual environment, the environment must be activated to use orthofisher.