<commit_before>##############################################################################
#   
#   Name:           Macaca_mulatta.ini
#   
#   Description:    Configuration file for Rhesus macaque ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

# Assembly info
ENSEMBL_CHROMOSOMES     = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 X MT ]

UCSC_GOLDEN_PATH        = rheMac2   ;
NCBI_GOLDEN_PATH     = 9544

SPECIES_RELEASE_VERSION = 10


# Search config
ENSEMBL_SEARCH_IDXS = [ Domain Gene GenomicAlignment Marker Sequence ]

ENSEMBL_GENOME_SIZE     = 0.25

##################
# DATABASE CONFIG
# Change the values to the local names of these databases
##################


[databases]
DATABASE_CORE            =    %_core_%
DATABASE_FUNCGEN         = %_funcgen_%
DATABASE_OTHERFEATURES =    %_otherfeatures_%
DATABASE_USERDATA  = macaca_mulatta_userdata

# You can overide the default settings (in DEFAULTS.ini) for specific
# databases. To do this, create an ini-file for this species e.g.
# public-plugins/mirror/conf/ini-file/Macaca_mulatta.ini with
# the section you wish to overwrite (see the example INI file:
# public-plugins/mirror/conf/ini-files/Genus_species.ini



####################
# Help Database Config
####################

[DATABASE_USERDATA]

[DATABASE_WEBSITE]

# Accept defaults


####################
# Species-specific colours
####################

[ENSEMBL_STYLE]

[ENSEMBL_COLOURS] 
# Accept defaults

[TAXON_LABEL]
# Accept defaults

####################
# Trace Config
####################

[ENSEMBL_SPECIES_TRACE_DATABASES]
# None


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini

[ENSEMBL_EXTERNAL_INDEXERS]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini



#############
# DAS CONFIG
#############
[ENSEMBL_TRACK_DAS_SOURCES]
# None
[ENSEMBL_INTERNAL_DAS_SOURCES]
# None

####################
# Configure External Genome Browsers
# EGB_TEST = Test external link
# KEY must be present in [ENSEMBL_EXTERNAL_URLS] section below which gives 
# the URL.... for the click - the entry here just gives the text link
####################

[EXTERNAL_GENOME_BROWSERS] 


####################
# Configure External URLs
# These are mainly for (1) External Genome Browse  {EGB_ }
#                      (2) DAS tracks              {DAS_ }
####################

[ENSEMBL_EXTERNAL_URLS]


[SAMPLE_DATA]
LOCATION_PARAM    = 4:82972301-83097692
LOCATION_TEXT     = 4:82972301-83097692

GENE_PARAM        = ENSMMUG00000000222
GENE_TEXT         = GLHA_MACMU

TRANSCRIPT_PARAM  = ENSMMUT00000000333
TRANSCRIPT_TEXT   = ENSMMUT00000000333

SEARCH_TEXT       = insulin receptor 

<commit_msg>new variation db for Macaca mulatta for release 67, author:tm6<commit_after>##############################################################################
#   
#   Name:           Macaca_mulatta.ini
#   
#   Description:    Configuration file for Rhesus macaque ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

# Assembly info
ENSEMBL_CHROMOSOMES     = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 X MT ]

UCSC_GOLDEN_PATH        = rheMac2   ;
NCBI_GOLDEN_PATH     = 9544

SPECIES_RELEASE_VERSION = 10


# Search config
ENSEMBL_SEARCH_IDXS = [ Domain Gene GenomicAlignment Marker Sequence ]

ENSEMBL_GENOME_SIZE     = 0.25

##################
# DATABASE CONFIG
# Change the values to the local names of these databases
##################


[databases]
DATABASE_CORE            =    %_core_%
DATABASE_FUNCGEN         = %_funcgen_%
DATABASE_OTHERFEATURES =    %_otherfeatures_%
DATABASE_VARIATION   = %_variation_%
DATABASE_USERDATA  = macaca_mulatta_userdata

# You can overide the default settings (in DEFAULTS.ini) for specific
# databases. To do this, create an ini-file for this species e.g.
# public-plugins/mirror/conf/ini-file/Macaca_mulatta.ini with
# the section you wish to overwrite (see the example INI file:
# public-plugins/mirror/conf/ini-files/Genus_species.ini



####################
# Help Database Config
####################

[DATABASE_USERDATA]

[DATABASE_WEBSITE]

# Accept defaults


####################
# Species-specific colours
####################

[ENSEMBL_STYLE]

[ENSEMBL_COLOURS] 
# Accept defaults

[TAXON_LABEL]
# Accept defaults

####################
# Trace Config
####################

[ENSEMBL_SPECIES_TRACE_DATABASES]
# None


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini

[ENSEMBL_EXTERNAL_INDEXERS]
; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini



#############
# DAS CONFIG
#############
[ENSEMBL_TRACK_DAS_SOURCES]
# None
[ENSEMBL_INTERNAL_DAS_SOURCES]
# None

####################
# Configure External Genome Browsers
# EGB_TEST = Test external link
# KEY must be present in [ENSEMBL_EXTERNAL_URLS] section below which gives 
# the URL.... for the click - the entry here just gives the text link
####################

[EXTERNAL_GENOME_BROWSERS] 


####################
# Configure External URLs
# These are mainly for (1) External Genome Browse  {EGB_ }
#                      (2) DAS tracks              {DAS_ }
####################

[ENSEMBL_EXTERNAL_URLS]


[SAMPLE_DATA]
LOCATION_PARAM    = 4:82972301-83097692
LOCATION_TEXT     = 4:82972301-83097692

GENE_PARAM        = ENSMMUG00000000222
GENE_TEXT         = GLHA_MACMU

VARIATION_PARAM   = rs194092193 
VARIATION_TEXT    = rs194092193


TRANSCRIPT_PARAM  = ENSMMUT00000000333
TRANSCRIPT_TEXT   = ENSMMUT00000000333

SEARCH_TEXT       = insulin receptor 


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