Installation¶
Automated Installation¶
This installation procedure assumes that you have a working perl version and a Miniconda installation.
- “Install” MIP
clone the official git repository $ git clone https://github.com/henrikstranneheim/MIP.git $ cd MIPAfter 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 bychmod +x file
.
- Create the install instructions for MIP
$ perl install.pl This will generate a batch script "mip.sh" for the install in your working directory.
- 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
- Run MIP
$ source activate mip $ mip.pl -h
Manual Installation¶
- Install a fresh copy of Perl
On UNIX, Perl5 can be installed by following these instructions. It uses Perlbrew.
- To switch to the new Perl installation, you might need to run:
$ INSTALLER_PERL_VERSION=5.16.0 $ perlbrew switch perl-$INSTALLER_PERL_VERSION
- “Install” MIP
clone the official git repository $ git clone https://github.com/henrikstranneheim/MIP.git $ cd MIP $ perl mip.pl -hAfter 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 bychmod +x file
.
- Dependencies
You need to make sure all depedencies are installed and loaded (See Setup). However, MIP should tell you if something is missing.
- To install the dependencies - use cpanm:
cpanm <dependency> $ cpanm YAML