###############################################################################
#   
#   Name:           Homo_sapiens.ini
#   
#   Description:    Configuration file for Human ensembl
#
###############################################################################

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

# Database info: only specify values if different from those in DEFAULTS

# Assembly info
ENSEMBL_CHROMOSOMES     = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT]
SPECIES_RELEASE_VERSION = 36b
ALTERNATIVE_ASSEMBLY    = VEGA

# Search config
; list of features that are indexed ready for searching
ENSEMBL_SEARCH_IDXS     = [ AffyProbe Domain Family Gene GenomicAlignment Marker SNP Sequence ]


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

[databases]

ENSEMBL_CDNA      = %_cdna_%
ENSEMBL_DB        = %_core_%
ENSEMBL_OTHERFEATURES       = %_otherfeatures_%
ENSEMBL_VARIATION = %_variation_%
ENSEMBL_VEGA      = %_vega_%

# 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/Homo_sapiens.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
####################

[ENSEMBL_WEBSITE] 
# Accept defaults


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

[ENSEMBL_STYLE]

[ENSEMBL_COLOURS]
# Accept defaults


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

[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults

[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults


#############
# DAS CONFIG
#############
# single sources used on a per-track only basis
[ENSEMBL_TRACK_DAS_SOURCES]

[ENSEMBL_INTERNAL_DAS_SOURCES]
; Example config - edit this and remove trailing ;
;sometrack = 1     ; Needed to add to zmenu by default

[sometrack]
;dsn = sometrack
;url = http://someserver:someport/das
;label = This is my track
;caption = Just alignments
;col = purple
;labelflag = U
;depth = 20
;group = 0
;description = just a config example
;on = [ protview geneview ]
;active = 1
;strand = b
;types= [ ]


####################
# Configure External Genome Browsers
####################

[EXTERNAL_GENOME_BROWSERS] 
EGB_UCSC         = UCSC browser
EGB_NCBI         = NCBI browser
# 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


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

[ENSEMBL_EXTERNAL_URLS]


DAS_SNPSTATUS  = http://hapmap.cshl.org/docs/snp_categories.html
DAS_ACEMBLY    = http://www.ncbi.nlm.nih.gov/AceView/av.cgi?db=30;q=###ID###
DAS_HSGENEID   = http://www1.imim.es/cgi-bin/das/das_genes_human.cgi?geneid=###ID###
DAS_HSSGP      = http://www1.imim.es/cgi-bin/das/das_genes_SGP_human.cgi?SGP=###ID###
DAS_HSTIGR     = http://www.tigr.org/docs/tigr-scripts/nhgi_scripts/tc_report.pl?species=human;tc=###ID###
DAS_NCBIGSCAN  = http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/GSfasta?label=###ID###
DAS_REFSEQ     = http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?Q=###ID###
DAS_NCBITRANS  = http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf&query=###ID###&qchr=&advsrch=off
DAS_ONCOVIEW   = http://www.sanger.ac.uk/perl/CGP/oncoview?;action=mutation;gene_name=###ID###
EGB_NCBI       = http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&CHR=###CHR###&BEG=###START###&END=###END###
EGB_UCSC       = http://genome.cse.ucsc.edu/cgi-bin/hgTracks?position=chr###CHR###%3A###START###-###END###;Submit=Submit;db=hg18
DOTS           = http://www.allgenes.org/allgenes/servlet?page=gene;id=###ID###
HVER121        = http://www.sanger.ac.uk/cgi-bin/microarrays/reporter_annotation?array_id=Hver1.2.1;reporter_id=###ID###
HVER131        = http://www.sanger.ac.uk/cgi-bin/microarrays/reporter_annotation?array_id=Hver1.3.1;reporter_id=###ID###
AFFY_HG_U133   = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834;id=###ID###
AFFY_HG_U95    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U133A   = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834;id=###ID###
AFFY_HG_U133B   = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834;id=###ID###
AFFY_HG_U133_ALL   = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834;id=###ID###
AFFY_HG_U95AV2  = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95A    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95B    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95C    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95D    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95E    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###
AFFY_HG_U95_ALL    = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834;id=###ID###

####################
# Configure blast data sources. 
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search 
# Accept defaults

[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults

[BLASTN_DATASOURCES]
# Sequence databases to use with search method (BLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ALL        = %_ 
CDNA_KNOWN      = %_
CDNA_NOVEL      = %_
CDNA_PSEUDO     = %_
CDNA_ABINITIO   = %_
CDNA_KNOWN-CCDS = %_
RNA_NC          = %_

[TBLASTX_DATASOURCES]
# Sequence databases to use with search method (TBLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ALL        = %_
CDNA_KNOWN      = %_
CDNA_NOVEL      = %_
CDNA_PSEUDO     = %_
CDNA_ABINITIO   = %_
CDNA_KNOWN-CCDS = %_
RNA_NC          = %_

[TBLASTN_DATASOURCES]
# Sequence databases to use with search method (TBLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = peptide
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ALL        = %_
CDNA_KNOWN      = %_
CDNA_NOVEL      = %_
CDNA_PSEUDO     = %_
CDNA_ABINITIO   = %_
CDNA_KNOWN-CCDS = %_
RNA_NC          = %_

[BLASTP_DATASOURCES]
# Sequence databases to use with search method (BLASTP)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = peptide
PEP_ALL         = %_
PEP_KNOWN       = %_
PEP_NOVEL       = %_
PEP_ABINITIO    = %_
PEP_KNOWN-CCDS  = %_

[BLASTX_DATASOURCES]
# Sequence databases to use with search method (BLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
PEP_ALL         = %_
PEP_KNOWN       = %_
PEP_NOVEL       = %_
PEP_ABINITIO    = %_
PEP_KNOWN-CCDS  = %_


[ENSEMBL_DICTIONARY]
strain = individual
                                                                                

####################
# Configure search example links
####################


[SEARCH_LINKS]
CONTIGVIEW1_TEXT   = AL138722.15.1.44776
CONTIGVIEW1_URL    = contigview?end=44776;region=AL138722.15.1.44776;start=101
CONTIGVIEW2_TEXT   = AL355340.17.1.112442
CONTIGVIEW2_URL    = contigview?end=112442;region=AL355340.17.1.112442;start=2001

CYTOVIEW1_TEXT   = AC016942.13.1.152014
CYTOVIEW1_URL    = cytoview?end=150014;region=AC016942.13.1.152014;start=1
CYTOVIEW2_TEXT   = AL139815.12.1.95016
CYTOVIEW2_URL    = cytoview?end=95016;region=AL139815.12.1.95016;start=1

DOMAINVIEW1_TEXT   = IPR006207
DOMAINVIEW1_URL    = domainview?domainentry=IPR006207
DOMAINVIEW2_TEXT   = IPR001811
DOMAINVIEW2_URL    = domainview?domainentry=IPR001811

EXONVIEW1_TEXT   = ENSE00001428812
EXONVIEW1_URL    = exonview?exon=ENSE00001428812
EXONVIEW2_TEXT   = ENSE00000837374
EXONVIEW2_URL    = exonview?exon=ENSE00000837374

FAMILYVIEW1_TEXT   = ENSF00000000045
FAMILYVIEW1_URL    = familyview?family=ENSF00000000045
FAMILYVIEW2_TEXT   = ENSF00000000105
FAMILYVIEW2_URL    = familyview?family=ENSF00000000105

FEATUREVIEW1_TEXT   = 230777_s_at
FEATUREVIEW1_URL    = featureview?id=230777_s_at;type=AffyProbe
FEATUREVIEW2_TEXT   = 235503_at
FEATUREVIEW2_URL    = featureview?id=235503_at;type=AffyProbe

GENEREGULATIONVIEW1_TEXT   = ENSG00000124334
GENEREGULATIONVIEW1_URL    = generegulationview?gene=ENSG00000124334
GENEREGULATIONVIEW2_TEXT   = ENSG00000102078
GENEREGULATIONVIEW2_URL    = generegulationview?gene=ENSG00000102078

GENESEQVIEW1_TEXT   = ENSG00000197587 ;DMBX1
GENESEQVIEW1_URL    = geneseqview?gene=ENSG00000197587
GENESEQVIEW2_TEXT   = ENSG00000139618 ;BRCA2
GENESEQVIEW2_URL    = geneseqview?gene=ENSG00000139618


GENESNPVIEW1_TEXT   = ENSG00000128573 ; FOXP2
GENESNPVIEW1_URL    = genesnpview?gene=ENSG00000128573
GENESNPVIEW2_TEXT   = ENSG00000139618 ; BRCA2
GENESNPVIEW2_URL    = genesnpview?gene=ENSG00000139618

GENESPLICEVIEW1_TEXT   = ENSG00000128573 ;FOXP2
GENESPLICEVIEW1_URL    = genespliceview?gene=ENSG00000128573
GENESPLICEVIEW2_TEXT   = ENSG00000084072 ;PPIE
GENESPLICEVIEW2_URL    = genespliceview?gene=ENSG00000084072

GENEVIEW1_TEXT   = ENSG00000139618 ;BRCA2
GENEVIEW1_URL    = geneview?gene=ENSG00000139618
GENEVIEW2_TEXT   = ENSG00000128573 ;FOXP2
GENEVIEW2_URL    = geneview?gene=ENSG00000128573

GOVIEW1_TEXT   = peptidyl-prolyl cis-trans isomerase activity
GOVIEW1_URL    = goview?query=peptidyl-prolyl cis-trans isomerase activity
GOVIEW2_TEXT   = guanine, xanthine and their nucleoside salvage
GOVIEW2_URL    = goview?query=guanine, xanthine and their nucleoside salvage

IDHISTORYVIEW1_TEXT   = ENSG00000139618
IDHISTORYVIEW1_URL    = idhistoryview?gene=ENSG00000139618
IDHISTORYVIEW2_TEXT   = ENST00000342929
IDHISTORYVIEW2_URL    = idhistoryview?transcript=ENST00000342929

KARYOVIEW1_TEXT
KARYOVIEW1_URL    = karyoview

LDTABLEVIEW1_TEXT   = rs11571658
LDTABLEVIEW1_URL    = ldtableview?_format=HTML;dump=ashtml;snp=rs11571658;bottom=%7Copt_pop_CSHL-HAPMAP%3AHapMap-JPT%3Aon%7C
LDTABLEVIEW2_TEXT   = rs1362
LDTABLEVIEW2_URL    = ldtableview?_format=HTML;dump=ashtml;snp=rs1362;bottom=%7Copt_pop_PERLEGEN%3AAFD_EUR_PANEL%3Aon

LDVIEW1_TEXT   = rs11571658
LDVIEW1_URL    = ldview?snp=rs11571658;bottom=%7Copt_pop_CSHL-HAPMAP%3AHapMap-JPT%3Aon
LDVIEW2_TEXT   = rs1362
LDVIEW2_URL    = ldview?snp=rs1362;bottom=%7Copt_pop_PERLEGEN%3AAFD_EUR_PANEL%3Aon

MAPVIEW1_TEXT   = 1
MAPVIEW1_URL    = mapview?chr=1
MAPVIEW2_TEXT   = MT
MAPVIEW2_URL    = mapview?chr=MT

MARKERVIEW1_TEXT   = ECD13863
MARKERVIEW1_URL    = markerview?marker=ECD13863
MARKERVIEW2_TEXT   = G43264
MARKERVIEW2_URL    = markerview?marker=G43264

PROTVIEW1_TEXT   = ENSP00000342827
PROTVIEW1_URL    = protview?peptide=ENSP00000342827
PROTVIEW2_TEXT   = ENSP00000328269
PROTVIEW2_URL    = protview?peptide=ENSP00000328269

SNPVIEW1_TEXT   = rs10264683
SNPVIEW1_URL    = snpview?snp=rs10264683
SNPVIEW2_TEXT   = rs11571658 ; BRCA2 in/del
SNPVIEW2_URL    = snpview?snp=rs11571658

SYNTENYVIEW1_TEXT   = 17 (with Dog)
SYNTENYVIEW1_URL    = syntenyview?chr=17;otherspecies=Canis_familiaris
SYNTENYVIEW2_TEXT   = X (with Mouse)
SYNTENYVIEW2_URL    = syntenyview?chr=X;otherspecies=Mus_musculus

TRANSVIEW1_TEXT   = ENST00000342929
TRANSVIEW1_URL    = transview?transcript=ENST00000342929
TRANSVIEW2_TEXT   = ENST00000365607
TRANSVIEW2_URL    = transview?transcript=ENST00000365607

DEFAULT1_TEXT   = AL138722.15.1.44776
DEFAULT1_URL    = contigview?end=44776;region=AL138722.15.1.44776;start=101

DEFAULT2_TEXT   = ENSG00000139618 ;BRCA2
DEFAULT2_URL    = geneview?gene=ENSG00000139618



## END SEARCH_LINKS - N.B. DO NOT DELETE THIS LINE!!!