Raw content of LowCoverageGeneBuildConf
<![CDATA[package LowCoverageGeneBuildConf;
use strict;
use vars qw( %LowCoverageGeneBuildConf );
# Notes: this is mammal-specific
%LowCoverageGeneBuildConf = (
# User-specific configuration:
LC_USER => '', #ba1
LC_GeneBuilderID => '', #4
LC_DATE => '', #YYYY-MM-Ensembl
LC_ASSEMBLY_NAME => '', #otoGar1, what broad calls the assembly
LC_ASSEMBLY_DATE => '', #YYYY-MM, when broad completed assembly
#perl5lib - this is the path to be added (temporarily) to the front of your perl5lib, make sure ensembl-config goes first
LC_PERL5LIB => '', #/ecs4/work1/sd3/rabbit1/ensembl-config/rabbit/rabbit_1.0:/ecs4/work1/sd3/rabbit1/ensembl/modules:/ecs4/work1/sd3/rabbit1/ensembl-pipeline/modules:/ecs4/work1/sd3/rabbit1/ensembl-analysis/modules:/ecs4/work1/sd3/rabbit1/ensembl-analysis/scripts/buildchecks:/ecs4/work1/sd3/rabbit1/ensembl-compara/modules:/ecs4/work1/sd3/rabbit1/ensembl-pipeline/scripts
LC_cvsDIR => '',#/nfs/acari/ba1/PerlCode/
LC_workDIR => '',#/lustre/work1/ba1/test/
LC_scratchDIR => '', #/lustre/scratch1/ba1/test/ Pipeline output directory
# Species-specific configuration:
LC_SPECIES => '',#armadillo
LC_BUILD_VERSION => '', #arma_1.0 in config dir eg. ensembl-config/armadillo/arma_1.0/
#data-specific cofiguration from BROAD and EBI
LC_AB_INITIO_LIB => '', #/ecs4/work1/sd3/rabbit1/repeat_libraries/ab_initio.lib
LC_SUPP_LIB => '', #/ecs4/work1/sd3/rabbit1/repeat_libraries/supplemental.lib
LC_ASSEMBLY_AGP => '', #/ecs4/work1/sd3/rabbit1/assembly/assembly.agp
LC_ASSEMBLY => '', #/ecs4/work1/sd3/rabbit1/assembly/assembly.bases #unzipped name
LC_SCAFFOLDS => '', #/ecs4/work1/sd3/rabbit1/assembly/scaffolds.fasta #unzipped name
# Taxonomy
# Not used any more (assembly name used instead)LC_DEFAULT => '', #RABBIT #use a short name (used for assembly) - look at ensj-healthcheck/src/org/ensembl/healthcheck/Species.java for ideas
LC_NAME => '', #Oryctolagus cuniculus #scientific name
TAXON_DBNAME => 'ncbi_taxonomy',
TAXON_DBHOST => 'ens-livemirror',
TAXON_DBPORT => '3306',
# database to put sequence and genes into
LC_DBNAME => '',#ba1_test_code
LC_DBHOST => '',#genebuild1
LC_DBUSER => '',#ensadmin
LC_DBPASS => '',
LC_DBPORT => '',#3306
LC_DBprefix => '',#ba1_test_
LC_DBro => '',#ensro
# if want the debug statements printed
LC_DEBUG => 1,
# Your choice of which RepeatMasks should be used for Pipeline
# This is decided upon <after> all 3 repeatMask analyses are run, and <before> the
# RepeatMask-dependent analyses are run
LC_REPMASK_CHOICE => [('RepeatMask','Supp_RepeatMask')], #[ ('RepeatMask','Supp_RepeatMask') ]
# Groups of analyses
LC_REPEATMASKS => [
{
logic_name => 'RepeatMask',
},
{
logic_name => 'Supp_RepeatMask',
},
{
logic_name => 'Ab_initio_RepeatMask',
}
],
LC_REPEATMASK_INDEPENDENT => [
{
logic_name => 'CpG',
},
{
logic_name => 'Dust',
},
{
logic_name => 'Eponine',
},
{
logic_name => 'TRF',
},
{
logic_name => 'tRNAscan',
},
{
},
],
LC_REPEATMASK_DEPENDENT => [
{
logic_name => 'Genscan',
},
{
logic_name => 'Unigene',
},
{
logic_name => 'Uniprot',
},
{
logic_name => 'Vertrna',
},
],
);
sub import {
my ($callpack) = caller(0); # Name of the calling package
my $pack = shift; # Need to move package off @_
# Get list of variables supplied, or else
# all of GeneConf:
my @vars = @_ ? @_ : keys( %LowCoverageGeneBuildConf );
return unless @vars;
# Predeclare global variables in calling package
eval "package $callpack; use vars qw("
. join(' ', map { '$'.$_ } @vars) . ")";
die $@ if $@;
foreach (@vars) {
if ( defined $LowCoverageGeneBuildConf{ $_ } ) {
no strict 'refs';
# Exporter does a similar job to the following
# statement, but for function names, not
# scalar variables:
*{"${callpack}::$_"} = \$LowCoverageGeneBuildConf{ $_ };
} else {
die "Error: LowCoverageGeneBuildConf: $_ not known\n";
}
}
}
1;
]]>