How to install Python 3 and required modules on macOS X

A detailed guide on our favorite way to locally install Python and the required packages on your local macOS X machine.

Install Homebrew

Homebrew is a package manager for macOS, much like apt-get on Linux. Please install this.

To install, simply open your Terminal and type:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Once you have Homebrew installed, open Terminal and type:

brew install python3

Download Muscle from:www.drive5.com/muscle/downloads.htm
Extract the file and copy to your cider-seq folder.
If placed in another folder, make sure you edit the path address in the ciderseq_config.json file.
For MAC OS, please edit the name of the MUSCLE file in the ciderseq_config.json file to muscle3.8.31_i86darwin64 or whichever version of MUSCLE you downloaded.

Download the latest blast .dmg file from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Double click on the downloaded file to install (required administrator account)

Open Terminal and type:

pip install [modulename]

for example:

pip install biopython

will install Biopython.

Please repeat and use pip to install all the required modules for ciderseq (see Readme)

Remember, if you already have Python 2 installed, use:

pip3 install [module]

to install the module on your Python 3 installation.

Similarly, to run python commands using Python 3, type:

python3 [command]

for example:

python3 ciderseq.py --format fastq examples/ciderseq_config.json examples/example1.fastq

will run ciderseq using Python 3, even if you have Python 2 also installed.