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ensembl-gh-mirror
ensembl-hive
Commits
cb96a1a2
Commit
cb96a1a2
authored
Oct 01, 2013
by
Leo Gordon
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newer Perl required, BioPerl no longer required, seed_pipeline.pl mentioned
parent
5f218bee
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docs/eHive_install_usage.txt
docs/eHive_install_usage.txt
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docs/eHive_install_usage.txt
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cb96a1a2
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@@ -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
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@@ -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 # o
ptional but recommended
, see 2.
7.
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules
# o
nly 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 # o
ptional but recommended
, see 2.
7.
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules
# o
nly 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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@@ -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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