Commit 3457eedc authored by Ian Longden's avatar Ian Longden
Browse files

use the registry to get the core and vega databses that way we dont have to...

use the registry to get the core and vega databses that way we dont have to remember to update this file for every release and changing the release number. You can still use the old way as well in case you have to, i.e. on different servers
parent 6129748a
......@@ -1016,7 +1016,7 @@ priority = 1
prio_descr = main
parser = GOSlimParser
release_uri =
data_uri = script:host=>ens-livemirror,dbname=>ensembl_ontology_56,
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_58,
[source GO::homo_sapiens]
......@@ -1114,17 +1114,6 @@ parser = HGNCParser
release_uri =
data_uri =
[source HGNC::homo_sapiens#08]
# used by #02
name = HGNC
download = N
order = 30
priority = 100
prio_descr = desc_only
parser = HGNCParser
release_uri =
data_uri =
[source HGNC::homo_sapiens]
# Used by homo_sapiens
name = HGNC
......@@ -1134,8 +1123,8 @@ priority = 1
prio_descr = havana
parser = HGNC_ENSTParser
release_uri =
data_uri = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b,
data_uri = script:
#data_uri = script:vhost=>ens-staging1,vdbname=>homo_sapiens_vega_58_37c,vport=>5306,vuser=>anonymous,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
[source HGNC::homo_sapiens#02]
......@@ -1147,7 +1136,7 @@ priority = 4
prio_descr = entrezgene_manual
parser = HGNCParser
release_uri =
data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
[source HGNC::homo_sapiens#03]
......@@ -1159,7 +1148,18 @@ priority = 5
prio_descr = refseq_manual
parser = HGNCParser
release_uri =
data_uri = file:HGNC/HGNC_TO_ENSG
data_uri =
[source HGNC::homo_sapiens#09]
# used by #02
name = HGNC
download = N
order = 30
priority = 5
prio_descr = swissprot_manual
parser = HGNCParser
release_uri =
data_uri =
[source HGNC::homo_sapiens#04]
# used by #02 which produces HGNC refseq and entrezgene types
......@@ -1170,7 +1170,7 @@ priority = 6
prio_descr = entrezgene_mapped
parser = HGNCParser
release_uri =
data_uri = file:HGNC/HGNC_TO_ENSG
data_uri =
[source HGNC::homo_sapiens#05]
# used by #02 which produces HGNC refseq and entrezgene types
......@@ -1181,7 +1181,7 @@ priority = 7
prio_descr = refseq_mapped
parser = HGNCParser
release_uri =
data_uri = file:HGNC/HGNC_TO_ENSG
data_uri =
[source HGNC::homo_sapiens#06]
# used by uniprotParser
......@@ -1194,6 +1194,17 @@ parser = uniprotparser
release_uri =
data_uri = see_uniprot
[source HGNC::homo_sapiens#08]
# used by #02
name = HGNC
download = N
order = 30
priority = 100
prio_descr = desc_only
parser = HGNCParser
release_uri =
data_uri =
[source IMGT/GENE_DB::homo_sapiens]
# Used by homo_sapiens
name = IMGT/GENE_DB
......@@ -1427,7 +1438,8 @@ priority = 1
prio_descr = vega
parser = MGI_Vega_Parser
release_uri =
data_uri = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j,
data_uri = script:
#data_uri = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
[source MGI::mus_musculus#03]
# Used by mus_musculus
......@@ -1481,7 +1493,7 @@ priority = 1
prio_descr =
parser = OTTTParser
release_uri =
data_uri = script:host=>ens-staging,port=>5317,dbname=>mus_musculus_vega_56_37i,
data_uri =
[source RGD::rattus_norvegicus]
# Used by rattus_norvegicus
......@@ -1599,7 +1611,7 @@ download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqParser
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Equus_caballus/RNA/rna.gbk.gz
......@@ -2353,7 +2365,8 @@ priority = 1
prio_descr =
parser = HGNC_curated_transcriptParser
release_uri =
data_uri = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b,
data_uri = script:
#data_uri = script:vhost=>ensembldb.ensembl.org,vport=>5306,vdbname=>homo_sapiens_vega_57_37b,vuser=>anonymous,vprot=>5306,chost=>ens-staging,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
[source HGNC_automatic_transcript::homo_sapiens]
......@@ -2391,7 +2404,8 @@ priority = 1
prio_descr =
parser = MGI_curated_transcriptParser
release_uri =
data_uri = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j,
data_uri = script:
#data_uri = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
[source MGI_curated_gene::mus_musculus]
name = MGI_curated_gene
......
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