Raw content of cDNAUpdate
<![CDATA[package cDNAUpdate;
=pod
=head1 NAME
cDNAupdate.pm
=head1 DESCRIPTION
This file contains the necessary configuration for running cDNA_update
for both human and mouse cDNAs. You should read this POD along with
the POD for cDNA_update for an overview of the cDNA_update process.
As in all configurations there is a default section containg all
variables that are required, followed by the individual settings for
human and mouse. Which species to use is set when cDNA_update.pl is
run.
Note that the import subroutine is slightly different to the method
usually used for importing the configurations as the cDNA_update
procedure itself doesn't follow a regular genebuild pipeline.
Some variables are pre-defined in the default section, these should
not require minimal modicifations once they have been set. The user
section will change every time the procedure is run.
=cut
use strict;
use vars qw(%Config);
%Config = (
DEFAULT => {
# Admin rights are required
WB_DBUSER => 'ensadmin',
WB_DBPASS => 'ensembl',
WB_REF_DBPORT => 3306,
# Path to gss file
GSS_PATH => '/ensembl-personal/genebuilders/cDNA_update/gss_acc.txt',
# Various scripts required by the process.
FASTA_SPLIT => '/nfs/acari/searle/progs/production_code/ensembl-trunk_1106/ensc-core/src/Programs/fastasplit',
POLYA_CLIPPING_PATH => '/ensembl-pipeline/scripts/EST/new_polyA_clipping.pl',
FIND_N_PATH => '/ensembl-pipeline/scripts/cDNA_update/find_N.pl',
STORE_UNMAPPED_PATH => '/ensembl-pipeline/scripts/cDNA_update/store_unmapped_cdnas.pl',
UNMAPPED_REASONS_PATH => '/ensembl/misc-scripts/unmapped_reason/unmapped_reason.txt',
LOAD_TAX_PATH => '/ensembl-pipeline/scripts/load_taxonomy.pl',
# Exonerate specifications
PROGRAM_NAME => "exonerate",
PROGRAM_VERSION => "0.9.0",
PROGRAM_FILE => "/usr/local/ensembl/bin/exonerate-0.9.0",
MODULE_NAME => "Exonerate2Genes",
# Source data files details
SOURCE_HOST => 'cbi4',
SOURCE_DIR => '/data/blastdb/',
# Taxonomy db for loading meta_table - should not need to change
TAXONDBNAME => 'ncbi_taxonomy',
TAXONDBHOST => 'ens-livemirror',
TAXONDBPORT => 3306,
# For the comparison only
OLD_FEATURE_NAME => 'cDNA_update',
# These variables need to be set, please do so in the
# corresponding hash tables for the species you want to
# analyse.
# User details
USER => '',
HOST => '',
GENEBUILD_ID => undef,
# Reference db (current build)
WB_REF_DBNAME => '',
WB_REF_DBHOST => '',
# New source db (PIPELINE)
WB_PIPE_DBNAME => '',
WB_PIPE_DBHOST => '',
WB_PIPE_DBPORT => 3306,
# New target db (ESTGENE)
WB_TARGET_DBNAME => '',
WB_TARGET_DBHOST => '',
WB_TARGET_DBPORT => 3306,
# Older cDNA db (needed for comparison only) -
# check schema is up to date!!!!!!
WB_LAST_DBNAME => '',
WB_LAST_DBHOST => '',
WB_LAST_DBPORT => undef,
# Reference db (last build, needed for comparison only)
WB_LAST_DNADBNAME => '',
WB_LAST_DNADBHOST => '',
WB_LAST_DNADBPORT => undef,
# Path to your cvs directory
CVS_DIR => '',
# Where the output files should go
DATA_DIR => '',
# Path to the genomic sequence
GENOMICSEQS => '',
# Chunk size recommendations: 5500 for human
# otherwise get AWOL jobs in first run
CHUNK => undef,
# Sequence files
VERTRNA => '',
VERTRNA_UPDATE => '',
REFSEQ => '',
# Species information
COMMON_SPECIES_NAME => '',
SPECIES => '',
TAX_ID => undef,
},
human => {
USER => 'amonida',
HOST => 'bc-9-1-01',
GENEBUILD_ID => 25,
WB_REF_DBNAME => 'amonida_human_core_55',
WB_REF_DBHOST => 'genebuild7',
WB_PIPE_DBNAME => 'amonida_homo_cdna0509_ref',
WB_PIPE_DBHOST => 'genebuild1',
WB_PIPE_DBPORT => 3306,
WB_TARGET_DBNAME => 'amonida_homo_cdna0509_update',
WB_TARGET_DBHOST => 'genebuild1',
WB_TARGET_DBPORT => 3306,
WB_LAST_DBNAME => 'homo_sapiens_cdna_54_36p',
WB_LAST_DBHOST => 'ens-livemirror',
WB_LAST_DBPORT => 3306,
WB_LAST_DNADBNAME => 'homo_sapiens_core_54_36p',
WB_LAST_DNADBHOST => 'ens-livemirror',
WB_LAST_DNADBPORT => 3306,
CVS_DIR => "$ENV{CVSDIR}",
DATA_DIR => "$ENV{WORK}",
# You shouldn't need to change the settings below but do check #
# that they are correct. #
################################################################
# Path to the genomic sequence
GENOMICSEQS => '/data/blastdb/Ensembl/Human/GRCh37/genome/softmasked/softmasked_dusted.fa',
# Chunk size recommendations: 5500 for human
# otherwise get AWOL jobs in first run
CHUNK => 5500,
# Sequence files
VERTRNA => 'embl_vertrna-1',
VERTRNA_UPDATE => 'emnew_vertrna-1',
# Using human sequence
REFSEQ => 'hs.fna',
# Species information
COMMON_SPECIES_NAME => 'human',
SPECIES => 'Homo sapiens',
TAX_ID => 9606,
},
mouse => {
USER => 'amonida',
HOST => 'bc-9-1-03',
GENEBUILD_ID => 25,
WB_REF_DBNAME => 'amonida_mouse_core_53',
WB_REF_DBHOST => 'genebuild4',
WB_PIPE_DBNAME => 'amonida_mus_test_ref',
WB_PIPE_DBHOST => 'genebuild4',
WB_PIPE_DBPORT => 3306,
WB_TARGET_DBNAME => 'amonida_mus_test_update',
WB_TARGET_DBHOST => 'genebuild4',
WB_TARGET_DBPORT => 3306,
WB_LAST_DBNAME => 'mus_musculus_cdna_53_37f',
WB_LAST_DBHOST => 'ensdb-archive',
WB_LAST_DBPORT => 5304,
WB_LAST_DNADBNAME => 'mus_musculus_core_53_37f',
WB_LAST_DNADBHOST => 'ens-livemirror',
WB_LAST_DNADBPORT => 3306,
CVS_DIR => '/nfs/acari/amonida/projects/cdna_update/mouse/',
DATA_DIR => "$ENV{SCRATCH}",
# You shouldn't need to change the settings below but do check #
# that they are correct. #
################################################################
# Path to the genomic sequence
GENOMICSEQS => '/data/blastdb/Ensembl/Mouse/NCBIM37/genome/softmasked_dusted/toplevel_sequence.fa',
# Chunk size recommendations: 1500 for mouse
# otherwise get AWOL jobs in first run
CHUNK => 1500,
# Sequence files
VERTRNA => 'embl_vertrna-1',
VERTRNA_UPDATE => 'emnew_vertrna-1',
REFSEQ => 'mouse.fna',
# Species information
COMMON_SPECIES_NAME => 'mouse',
SPECIES => 'Mus musculus',
TAX_ID => 10090,
}
);
sub import {
my ($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 General:
my @vars = @_ ? @_ : keys( %Config );
return unless @vars;
# Predeclare global variables in calling package
eval "package $callpack; use vars qw("
. join(' ', map { '$'.$_ } @vars) . ")";
die $@ if $@;
foreach my $var (@vars) {
if ( defined $Config{ $var } ) {
no strict 'refs';
foreach my $key (keys %{$Config{$var}}) {
# Exporter does a similar job to the following
# statement, but for function names, not
# scalar variables:
*{"${callpack}::$key"} = \$Config{$var}{$key};
}
} else {
die "Error: Config: $var not known\n";
}
}
}
1;
]]>