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Installation

Prerequisite software

  • Mash >= v2.0
  • SQLite3 Removed in version 1.4
  • Perl
    • multithreading
    • BioPerl library
    • DBD::SQLite Removed in version 1.4
  • Quicktree

Environment

Environment variables

For most Linux OSs, you will need to set up your environment like this:

export PATH=$HOME/bin:$PATH
export PERL5LIB=$PERL5LIB:$HOME/lib/perl5

System packages

Some system packages are needed. On Ubuntu, this is how you might install these packages.

apt update
apt install -y build-essential cpanminus libexpat1-dev wget

Perl packages

There are some perl packages too and so this is how you would install those on most Linux OSs:

cpanm -l ~ --notest BioPerl Bio::Sketch::Mash

Quicktree

mkdir -pv $HOME/bin/build
cd $HOME/bin/build
wget https://github.com/khowe/quicktree/archive/v2.5.tar.gz
tar xvf v2.5.tar.gz 
cd quicktree-2.5
make
mv quicktree $HOME/bin/

Mash

mkdir -pv $HOME/bin/build
cd $HOME/bin/build
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
tar xvf mash-Linux64-v2.2.tar
mv -v mash-Linux64-v2.2/mash $HOME/bin/

Mashtree Installation from CPAN

Installing from CPAN installs the latest stable version of Mashtree. This method adds the Mashtree perl modules to the correct place in your home directory and adds the executables to your home bin directory.

export PERL5LIB=$PERL5LIB:$HOME/lib/perl5
cpanm -l ~ Mashtree
mashtree --help # verify it shows usage and not an error

Uninstallation from CPAN

cpanm --uninstall Mashtree --local-lib=$HOME

Other sources for Mashtree

Other instances of Mashtree can be found in the wild. Although I did not create these, others have found them useful. I cannot provide support for these outside instances.

Docker

Conda