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Installation

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Jennifer Chang edited this page Nov 20, 2019 · 3 revisions

First you will need to have some kind of shell and the following programs already installed:

If properly installed on your path, the programs should be available by typing which and the name of the program in your terminal.

**example

which blastn

# /usr/local/bin/blastn

which pip3

# /anaconda3/bin/pip

Each dependency provides its own instructions across operating system.

Downloading octoFLU

git clone https://github.com/flu-crew/octoFLU.git

Download smof

# if you have commandline python
pip install smof

# if you have anaconda python
conda install smof

smof is a python package for providing unix-like functions to search, sample, and reformat fasta files.

Within the octoFLU folder, edit the pipeline.sh to fill in the paths using which command.

BLASTN=/usr/local/bin/blastn
MAKEBLASTDB=/usr/local/bin/makeblastdb
SMOF=/anaconda3/bin/smof
MAFFT=/usr/local/bin/mafft
FASTTREE=/usr/local/bin/FastTreeMP
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