Installation

Automated Installation

This installation procedure assumes that you have a working perl version and a Miniconda installation.

  1. “Install” MIP
clone the official git repository
$ git clone https://github.com/henrikstranneheim/MIP.git
$ cd MIP

After this you can decide whether to make MIP an “executable” by either adding the install directory to the $PATH in e.g. “~/.bash_profile” or move all the files from this directory to somewhere already in your path like “~/usr/bin”. Remember to make the file(s) executable by chmod +x file.

  1. Create the install instructions for MIP
$ perl install.pl
This will generate a batch script "mip.sh" for the install in your working directory.
  1. Run the bash script
$ bash mip.sh
This will install all the dependencies of MIP and other modules included in MIP into a conda environment (defaults to "mip").
However a fresh version of perl and cpanm is installed outside of the conda environment, but are activated through bashrc and  bash_profile.

Note

This will add the following lines to bashrc and bash_profile if the install perl version is not found in your path:

'export PATH=$HOME/perl-PERLVERSION/:$PATH' >> ~/.bashrc
'eval `perl -I ~/perl-PERLVERSION/lib/perl5/ -Mlocal::lib=~/perl-PERLVERSION/`' >> ~/.bash_profile
'export PERL_UNICODE=SAD' >> ~/.bash_profile
  1. Run MIP
$ source activate mip
$ mip.pl -h

Manual Installation

  1. Install a fresh copy of Perl
On UNIX, Perl5 can be installed by following these instructions. It uses Perlbrew.
  1. To switch to the new Perl installation, you might need to run:
$ INSTALLER_PERL_VERSION=5.16.0
$ perlbrew switch perl-$INSTALLER_PERL_VERSION
  1. “Install” MIP
clone the official git repository
$ git clone https://github.com/henrikstranneheim/MIP.git
$ cd MIP
$ perl mip.pl -h

After this you can decide whether to make MIP an “executable” by either adding the install directory to the $PATH in e.g. “~/.bash_profile” or move all the files from this directory to somewhere already in your path like “~/usr/bin”. Remember to make the file(s) executable by chmod +x file.

  1. Dependencies
You need to make sure all depedencies are installed and loaded (See Setup). However, MIP should tell you if something is missing.
  1. To install the dependencies - use cpanm:
cpanm <dependency>
$ cpanm YAML