Installing lots of command line tools requires navigating a certain level of command-line bullshittery wizardry (source). Here are some tips intended to help you get up and running on a Mac.
First things first: Mac users should install command-line tools using the following command:
xcode-select --install
Homebrew
Homebrew isn't used by banzai, but installing it will make your life MUCH easier. Homebrew allows you to download and install a large number of tools right from the command line, avoiding many of the hassles. Install Homebrew in one easy go:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
PEAR
brew install homebrew/science/pear
vsearch
either:
brew install https://raw.githubusercontent.com/tseemann/homebrew-science/f55e38c5c941f8cf6db68cd576baafc6a1d89b1e/vsearch.rb
or
Download binary for v1.4.0
cp /Users/jimmy.odonnell/Applications/install/vsearch-1.4.0-osx-x86_64/bin/vsearch /usr/bin
mv /Users/jimmy.odonnell/Applications/install/vsearch-1.4.0-osx-x86_64/man/vsearch.1.gz /usr/share/man/man1/
cutadapt
Mysteriously disappeared from Jimmy's work computer (! AHA ! I think because I used pip, which was installed by Anaconda, which I then moved!), and Homebrew installation (brew install cutadapt) appeared broken as of 2015-10-19. To fix it, used easy_install, a python package managing tool that may or may not be automatically included in Mac python:
easy_install cutadapt
pip install cutadapt
seqtk
brew install seqtk
or, download the compressed file, unzip, cd into it, then
make
cp /Users/jimmy.odonnell/Downloads/seqtk-master/seqtk /usr/bin
swarm
cd /Users/jimmy.odonnell/Applications/install/swarm-master/src
make (requires gcc)
cp ../bin/swarm /usr/bin/swarm
cd ../man
gzip -c swarm.1 > swarm.1.gz
mv swarm.1.gz /usr/share/man/man1/
blast+
brew install homebrew/science/blast
pigz
Download .tar.gz file. Double-click to decompress it. cd it the new folder. Type:
make
then
cp /Users/jimmy.odonnell/Applications/pigz-2.3.3/pigz /usr/bin
fastqc
unpack dmg file into your Applications folder.
create symbolic link:
ln -s /Applications/FastQC.app/Contents/Resources/Java/fastqc /usr/bin/fastqc
MEGAN
You're on your own here.
usearch
(no longer required)
cp /Users/jimmy.odonnell/Downloads/usearch8.1.1756_i86osx32 /usr/bin/usearch
R
Self-explanatory.