Commit cb96a1a2 authored by Leo Gordon's avatar Leo Gordon
Browse files

newer Perl required, BioPerl no longer required, seed_pipeline.pl mentioned

parent 5f218bee
......@@ -2,7 +2,7 @@
1. Download and install the necessary external software:
1.1. Perl 5.6 or higher, since eHive code is written in Perl
1.1. Perl 5.10 or higher, since eHive code is written in Perl
# see http://www.perl.com/download.csp
......@@ -46,47 +46,37 @@ It will be convenient to set a variable pointing at this directory for future us
$ cd $ENSEMBL_CVS_ROOT_DIR
2.3. Log into the BioPerl CVS server (using "cvs" for password):
$ cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl login
# see http://www.bioperl.org/wiki/Using_CVS
2.4. Export the bioperl-live package:
$ cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl export bioperl-live
2.5. Log into the EnsEMBL CVS server at Sanger (using "CVSUSER" for password):
2.3. Log into the EnsEMBL CVS server at Sanger (using "CVSUSER" for password):
$ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl login
Logging in to :pserver:cvsuser@cvs.sanger.ac.uk:2401/cvsroot/ensembl
CVS password: CVSUSER
2.6. Export ensembl and ensembl-hive CVS modules:
2.4. Export ensembl and ensembl-hive CVS modules:
$ 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
2.7. In the likely case you are going to use eHive in the context of Compara pipelines,
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
2.8. Add new packages to the PERL5LIB variable:
2.6. Add new packages to the PERL5LIB variable:
# using bash syntax:
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live
$ 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 # optional but recommended, see 2.7.
$ 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
$ 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 # optional but recommended, see 2.7.
$ 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)
......@@ -98,6 +88,8 @@ It will be convenient to set a variable pointing at this directory for future us
* init_pipeline.pl is used to create hive databases, populate hive-specific and pipeline-specific tables and load data
* seed_pipeline.pl is used to add new jobs to the pipeline.
* beekeeper.pl is used to run the pipeline; send 'Workers' to the 'Meadow' to run the jobs of the pipeline
3.2 In ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig we keep example pipeline configuration modules that can be used by init_pipeline.pl .
......
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