orthofisher 0.0.3

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

For detailed instructions on usage and a tutorial, please see the online documentation.

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 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, the virtual environment must be activated to use orthofisher.