Commit ef21ba28 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Updated the list of dependencies

parent 3923647b
......@@ -4,30 +4,47 @@
1.1. Perl 5.10 or higher, since eHive code is written in Perl
# see http://www.perl.com/download.csp
see http://www.perl.com/download.csp
1.2. MySQL 5.1 or higher
1.2. A database engine of your choice
eHive keeps its state in a MySQL database, so you will need
(1) a MySQL server installed on the machine where you want to maintain the state and
(2) MySQL clients installed on the machines where the jobs are to be executed.
MySQL version 5.1 or higher is recommended to maintain compatibility with Compara pipelines.
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 and
(2) clients installed on the machines where the jobs are to be executed.
At the moment, the following engines are supported:
1.2.1. MySQL 5.1 or higher
see http://dev.mysql.com/downloads/
1.2.2. SQLite 3.6 or higher
see http://www.sqlite.org/download.html
1.2.3. PostgreSQL 9.2 or higher
see http://www.postgresql.org/download/
1.3. Perl DBI API version 1.6 or higher
Perl database interface that includes API to MySQL
Perl database interface that includes API to your desired database engine
see http://dbi.perl.org/
1.4. Perl libraries for visualisation (optional)
# see http://dbi.perl.org/
You can find them on CPAN:
- GraphViz (needed for generate_graph.pl)
- Chart::Gnuplot (needed for generate_timeline.pl)
2. Download and install essential and optional packages from BioPerl and EnsEMBL CVS
2. Download and install essential packages from EnsEMBL CVS
2.1. It is advised to have a dedicated directory where EnsEMBL-related packages will be deployed.
Unlike DBI modules that can be installed system-wide by the system administrator,
you will benefit from full (read+write) access to the EnsEMBL files/directories,
so it is best to install them under your home directory. For example,
$ mkdir $HOME/ensembl_main
It will be convenient to set a variable pointing at this directory for future use:
......@@ -57,26 +74,18 @@ It will be convenient to set a variable pointing at this directory for future us
$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout ensembl
$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout ensembl-hive
2.5. In the likely case you are going to use eHive in the context of Compara pipelines,
you will also need to install ensembl-compara:
$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout ensembl-compara
2.6. Add new packages to the PERL5LIB variable:
2.5. Add new packages to the PERL5LIB variable:
# using bash syntax:
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live # optional for eHive, but may be needed for EnsEMBL
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # only needed if you are planning to run Compara pipelines, see 2.5
#
# (for best results, append these lines to your ~/.bashrc configuration file)
# using [t]csh syntax:
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live # optional for eHive, but may be needed for EnsEMBL
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # only needed if you are planning to run Compara pipelines, see 2.5
#
# (for best results, append these lines to your ~/.cshrc or ~/.tcshrc configuration file)
......
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