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Update links to release 93
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Laurent Gil committed Apr 9, 2018
1 parent 6437cbf commit 0b1784c
Showing 1 changed file with 33 additions and 33 deletions.
66 changes: 33 additions & 33 deletions plugin_config.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ my $VEP_PLUGIN_CONFIG = {
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/dbNSFP.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/dbNSFP.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
Expand Down Expand Up @@ -301,7 +301,7 @@ my $VEP_PLUGIN_CONFIG = {
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Combined Annotation Dependent Depletion (CADD) is a tool for scoring the deleteriousness of single nucleotide variants and insertion/deletion variants in the human genome. CADD integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/CADD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/CADD.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -323,7 +323,7 @@ my $VEP_PLUGIN_CONFIG = {
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/FATHMM_MKL.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/FATHMM_MKL.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand Down Expand Up @@ -377,7 +377,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Carol.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Carol.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -395,7 +395,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Condel.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Condel.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
Expand Down Expand Up @@ -443,7 +443,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/LoFtool.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/LoFtool.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -461,7 +461,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/ExACpLI.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/ExACpLI.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -479,7 +479,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/MPC.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/MPC.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -497,7 +497,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/MTR.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/MTR.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -515,7 +515,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/REVEL.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/REVEL.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -538,7 +538,7 @@ my $VEP_PLUGIN_CONFIG = {
"enabled" => 0,
"section" => "Splicing predictions",
"helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/dbscSNV.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/dbscSNV.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
Expand All @@ -557,7 +557,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/GeneSplicer.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/GeneSplicer.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -577,7 +577,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/MaxEntScan.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/MaxEntScan.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -595,7 +595,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/SpliceRegion.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/SpliceRegion.pm",
},


Expand All @@ -610,7 +610,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Blosum62.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Blosum62.pm",
},

# Conservation
Expand All @@ -632,7 +632,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Conservation.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Conservation.pm",
"params" => [
"@*"
],
Expand Down Expand Up @@ -668,13 +668,13 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/AncestralAllele.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/AncestralAllele.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/homo_sapiens_ancestor_GRCh38_e92.fa.gz"
# "/path/to/homo_sapiens_ancestor_GRCh38_e93.fa.gz"
]
},

Expand All @@ -689,7 +689,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Identifiers",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/CSN.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/CSN.pm",
},


Expand All @@ -703,7 +703,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Reports allele frequencies from the Exome Aggregation Consortium",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/ExAC.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/ExAC.pm",
"section" => "Frequency data",
"requires_data" => 1,
"species" => [
Expand All @@ -725,7 +725,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Determines where in the secondary structure of a miRNA a variant falls",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/miRNA.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/miRNA.pm",
},


Expand All @@ -737,7 +737,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Finds the nearest gene to non-genic variants",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/NearestGene.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/NearestGene.pm",
},

# LD
Expand All @@ -747,7 +747,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/LD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/LD.pm",
"section" => "Variant data",
"params" => [
"@*"
Expand Down Expand Up @@ -803,7 +803,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Reports existing variants that fall in the same codon",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/SameCodon.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/SameCodon.pm",
"section" => "Variant data",
},
# LOVD
Expand All @@ -813,7 +813,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Retrieves LOVD variation data",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/LOVD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/LOVD.pm",
"section" => "Variant data",
},

Expand All @@ -824,7 +824,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/GO.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/GO.pm",
"section" => "Gene data",
},

Expand All @@ -835,7 +835,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Downstream.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Downstream.pm",
},

# ProteinSeqs
Expand All @@ -845,7 +845,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/ProteinSeqs.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/ProteinSeqs.pm",
},

# TSSDistance
Expand All @@ -855,7 +855,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Calculates the distance from the transcription start site for upstream variants ",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/TSSDistance.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/TSSDistance.pm",
},

# Phenotypes
Expand All @@ -865,7 +865,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Retrieves overlapping phenotype annotations",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Phenotypes.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Phenotypes.pm",
},
# Draw
{
Expand All @@ -875,7 +875,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"requires_install" => 1,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/Draw.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Draw.pm",
},
# G2P
{
Expand All @@ -885,7 +885,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"requires_data" => 1,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/G2P.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/G2P.pm",
},

# LocalID
Expand All @@ -895,7 +895,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Allows you to use variant IDs as VEP input without making a database connection.",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/92/LocalID.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/LocalID.pm",
},


Expand Down

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