eHive installation and setup

1. Perl 5.14 or higher
2. A database engine of your choice. eHive keeps its state in a database, so you will need
   1. a server installed on the machine where you want to maintain the state of your pipeline(s) and
   2. clients installed on the machines where the jobs are to be executed.
   At the moment, the following database options are available:
   • MySQL 5.1 or higher
   • SQLite 3.6 or higher
   • PostgreSQL 9.2 or higher
3. Perl DBI API version 1.6 or higher -- Perl database interface that has to include a driver for the database engine of your choice above.
4. Perl libraries for visualisation (optional but recommended). They can be found on CPAN:
   • GraphViz (needed for generate_graph.pl and the GUI)
   • Chart::Gnuplot (needed for generate_timeline.pl)

Check out the repository by cloning it from GitHub:

All eHive pipelines will require the ensembl-hive repository, which can be found on GitHub. As such it is assumed that Git is installed on your system, if not follow the instructions here

To download the repository, move to a suitable directory and run the following on the command line:

        git clone -b version/2.2 https://github.com/Ensembl/ensembl-hive.git

This will create ensembl-hive directory with all the code and documentation.
If you cd into the ensembl-hive directory and do an ls you should see something like the following:

        ls
        Changelog  docs  hive_config.json  modules  README.md  scripts  sql  t

modules

This contains all the eHive modules, which are written in Perl

scripts

Has various scripts that are key to initialising, running and debugging the pipeline

sql

Contains sql used to build a standard pipeline database

Optional configuration of the system:

You may find it convenient (although it is not necessary) to add "ensembl-hive/scripts" to your $PATH variable to make it easier to run beekeeper.pl and other useful Hive scripts.

• using bash syntax:

          export PATH=$PATH:$ENSEMBL_CVS_ROOT_DIR/ensembl-hive/scripts
                  #
                  # (for best results, append this line to your ~/.bashrc or ~/.bash_profile configuration file)
  

• using [t]csh syntax:

          set path = ( $path ${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/scripts )
                  #
                  # (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file)
  

Also, if you are developing the code and not just running ready pipelines, you may find it convenient to add "ensembl-hive/modules" to your $PERL5LIB variable.

• using bash syntax:

          export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
          export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
                  #
                  # (for best results, append these lines to your ~/.bashrc or ~/.bash_profile configuration file)
  

• using [t]csh syntax:

          setenv PERL5LIB  ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
          setenv PERL5LIB  ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
                  #
                  # (for best results, append these lines to your ~/.cshrc or ~/.tcshrc configuration file)