old_port_install_script.sh

#! /bin/bash
# install dependencies

sudo port install jpeg
sudo port install jpeg2ps
sudo port install libpng
sudo port install gd2
sudo port install fontconfig
sudo port install freetype
sudo port install raxml
sudo port install py26-ete2
sudo port install tophat
sudo port install cufflinks
sudo port install mongodb
sudo port install mysql5
sudo port install gcc_select
sudo port install libgcc
sudo port install py-biopython
sudo port install py-gitpython
sudo port install ipython
sudo port install py-pythonutils
sudo port install rb-bioruby
sudo port install ruby
sudo port install py-matplotlib
sudo port install py-pandas
sudo port install py-scipy
sudo port install py-numpy
sudo port install jpeg6b
sudo port install libjpeg-turbo
sudo port install perl
sudo port install gsl
sudo port install py27-gsl
sudo port install py-pip

brew tap homebrew/science
brew install abyss
brew install allpaths-lg
brew install amos
brew install bamtools
brew install bam-readcount
brew install --HEAD beagle
brew install bamutil
brew install bedops
brew install bedtools
brew install --HEAD bioawk
brew install bitseq
brew install blasr
brew install blast
brew install blat
brew install bowtie
brew install bowtie2
brew install bwa
brew install cd-hit
brew install celera-assembler
brew install clustal-omega
brew install clustal-w
brew install cufflinks
brew install fast-statistical-alignment
brew install fasta
brew install fastqc
brew install fasttree
brew install fastx-toolkit
brew install glimmer3
brew install hmmer
brew install igv
brew install infernal
brew install jellyfish
brew install kalign
brew install kissplice
brew install kmergenie
brew install lastz
brew install libsequence
brew install mafft
brew install minia
brew install mira
brew install mummer
brew install muscle
brew install novoalign
brew install paml
brew install phylip
brew install phyml
brew install primer3
brew install quast
brew install raxml
brew install samtools
brew install seqtk
brew install shogun
brew install sickle
brew install snp_sites
brew install soapdenovo
brew install spades
brew install sratoolkit
brew install stacks
brew install trinity
brew install trnascan
brew install velvet
brew install velvetoptimiser
brew install viennarna
brew install vcftools
brew install yaha

# brew install megahit