orthofisher 0.0.0

orthofisher

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Orthofisher conducts automated and high-throughout identification of a predetermined set of orthologs, which can be used for phylgenomics, gene family copy number determination and more!

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Quick Start

To ensure users are able to install orthofisher using a workflow they are familiar with, orthofisher is available for download from GitHub, PyPi, and the Anaconda cloud. However, before installing orthofisher, please first install HMMER3.

1) Prerequisite

Before installing orthofisher, please first install HMMER3 and add the 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 from source, we strongly recommend using a virtual environment. To do so, use the following commands:

# download
git clone https://github.com/JLSteenwyk/orthofisher.git
cd orthofisher/
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install
make install

To deactivate your virtual environment, use the following command:

# deactivate virtual environment
deactivate

Note, the virtual environment must be activated to use orthofisher.