InstallationLinuxSourceHPC

These instructions apply to version 2.99_001 and later.

These instructions assume you are not installing the GUI components. It is possible to run the GUI on HPC, and details can be added if needed.

They are based on development on Centos 6.3, but have not been tested line by line when written. Please report any errors or suggestions.

They also assume you are using a standard user account, and are accessing Biodiverse through the git repository.

Table of contents:

• Installation
  • Part 1. Install a non-system perl
  • Part 2. Clone the Biodiverse repo
  • Part 3. Install the perl dependencies

Installation

Part 1. Install a non-system perl

• Install PerlBrew, including its optional cpanm client.
  • Instructions are at https://perlbrew.pl/
  • You should not use the system perl. The operating system assumes specific versions of files are in the system perl.
  • Perlbrew is recommended, and is used for Biodiverse development, and is assumed below. There are other other systems like plenv which will likely also work, but I have not tested them.
  • Make sure you are using the non-system perl for all subsequent steps. This could involve adding a line to your .bashrc (or equivalent) file to ensure it is loaded each time you login. Perlbrew provides instructions on how to do this.

Part 2. Clone the Biodiverse repo

  #  update this if you wish to install to a different location or checkout a release tag
  git clone https://github.com/shawnlaffan/biodiverse.git

  #  the next section assumes you are in the biodiverse git directory
  cd biodiverse 

Part 3. Install the perl dependencies

  ##  if you are using perlbrew and forgot to install the cpanm client:
  perlbrew install-cpanm

  ## Alien::gdal is a big dependency.  It is listed in the cpanfile, 
  #  but it can be useful to install it first.
  #  Note that, if you have GDAL version 3.0 or higher already 
  #  installed on your system then this will use that version 
  #  instead of building its own.
  #  Note also that if you have loaded a system GDAL using ```module load``` 
  #  or similar then you need to ensure it is loaded each time 
  #  you run Biodiverse or it will fail to start.
  cpanm Alien::sqlite
  cpanm Alien::proj
  cpanm Alien::geos::af
  cpanm Alien::gdal

  #  Geo::GDAL::FFI does not yet declare this dependency
  cpanm FFI::Platypus::Declare
  
  ## Now install the rest of the dependencies
  ## Note that new deps might be added as 
  ## part of the development process
  cpanm --installdeps . 

  #  only if you are installing version 3.1 or earlier
  cpanm Task::Biodiverse::NoGUI

  ## some libs to make Biodiverse go faster
  ## Panda::Lib does not install on Windows, so is not in the generic dep list
  ## cpanm Panda::Lib
  cpanm Data::Recursive
  ##  Biodiverse::Utils is not yet on cpan
  cpanm https://github.com/shawnlaffan/biodiverse-utils/releases/download/v1.09/Biodiverse-Utils-1.09.tar.gz

  ##  if the above command fails with an error 
  #   regarding curl and libffi then use your
  #   system package manager to install libffi
  #   and then re-run the above command

Testing it

Follow these steps to check that everything is installed and Biodiverse will run.

  #  Make sure you are in the top level of the biodiverse distribution
  #  You should see directories bin, etc, lib, t, xt and so forth when you run ls.  
  export BD_NO_TEST_GUI=1  #  no need to test the GUI libs load
  prove -l

Running it

• Run your scripts as you would any other perl script, e.g.

perl ~/biodiverse/bin/run_randomisation.pl

Troubleshooting

• If you are keeping up with the git development then you will occassionally need to install extra dependencies.
  If perl complains that you are missing a module then it can be installed using cpanm. For example if the missing module is called Blort::Bork, then you can run cpanm Blort::Bork at the command line to install it and its dependencies.
• Please report any issues using the project issue tracker