dependencies.md

November 2, 2019 ยท View on GitHub

Guide to installing MMSEQ dependencies

  • Boost C++ Libraries
    • Mac OS X+MacPorts: port install boost
    • Mac OS X+Homebrew: brew install boost; ln -s /usr/local/lib/libboost_regex-mt.a /usr/local/lib/libboost_regex.a; ln -s /usr/local/lib/libboost_iostreams-mt.a /usr/local/lib/libboost_iostreams.a
    • Ubuntu/Debian/etc: apt-get install libboost-all-dev
    • Fedora/CentOS/Red Hat/etc: yum install boost (or, on older systems, yum install boost141)
  • GNU Scientific Library
    • Mac OS X+MacPorts: port install gsl
    • Mac OS X+Homebrew: brew install gsl
    • Ubuntu/Debian/etc: apt-get install libgsl0-dev
    • Fedora/CentOS/Red Hat/etc: yum install gsl
  • Armadillo C++ linear algebra library
    • Mac OS X+Homebrew: brew install homebrew/science/openblas; brew install homebrew/dupes/lapack; brew install armadillo
  • HTSlib library
    • Mac OS X+Homebrew: brew install htslib

Note that due to a lack of OpenMP support in Apple's clang compiler (as of El Capitan), the Mac binaries will be single-threaded.

Make sure you have a Ruby interpreter to run the Ruby scripts:

  • Ubuntu/Debian/etc: apt-get install ruby-full
  • Fedora/CentOS/Red Hat/etc: yum install ruby

To correct the transcript lengths for non-uniformity effects using the Poisson regression method of Li et al., install the R package mseq.