Skip to content

Commit

Permalink
Update for release 95
Browse files Browse the repository at this point in the history
  • Loading branch information
@ima23
ima23 committed Nov 1, 2018
1 parent ea716fe commit 663933b
Showing 1 changed file with 32 additions and 32 deletions.
64 changes: 32 additions & 32 deletions plugin_config.txt
View file
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/94/dbNSFP.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/CADD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/FATHMM_MKL.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/Carol.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/Condel.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/LoFtool.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/ExACpLI.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/MPC.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/MTR.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/REVEL.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/dbscSNV.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/GeneSplicer.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/MaxEntScan.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/SpliceRegion.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/Blosum62.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/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/94/Conservation.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/Conservation.pm",
"params" => [
"@*"
],
Expand Down Expand Up @@ -668,7 +668,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/AncestralAllele.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/AncestralAllele.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
Expand All @@ -689,7 +689,7 @@ 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/94/ExAC.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/ExAC.pm",
"section" => "Frequency data",
"requires_data" => 1,
"species" => [
Expand All @@ -710,7 +710,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CSN.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/CSN.pm",
},

# miRNA
Expand All @@ -720,7 +720,7 @@ 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/94/miRNA.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/miRNA.pm",
},


Expand All @@ -732,7 +732,7 @@ 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/94/NearestGene.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/NearestGene.pm",
},

# LD
Expand All @@ -742,7 +742,7 @@ 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/94/LD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/LD.pm",
"section" => "Variant data",
"params" => [
"@*"
Expand Down Expand Up @@ -798,7 +798,7 @@ 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/94/SameCodon.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/SameCodon.pm",
"section" => "Variant data",
},
# LOVD
Expand All @@ -808,7 +808,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Retrieves LOVD variation data",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LOVD.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/LOVD.pm",
"section" => "Variant data",
},

Expand All @@ -819,7 +819,7 @@ 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/94/GO.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/GO.pm",
"section" => "Gene data",
},

Expand All @@ -830,7 +830,7 @@ 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/94/Downstream.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/Downstream.pm",
},

# ProteinSeqs
Expand All @@ -840,7 +840,7 @@ 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/94/ProteinSeqs.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/ProteinSeqs.pm",
},

# TSSDistance
Expand All @@ -850,7 +850,7 @@ 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/94/TSSDistance.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/TSSDistance.pm",
},

# Phenotypes
Expand All @@ -860,7 +860,7 @@ my $VEP_PLUGIN_CONFIG = {
"helptip" => "Retrieves overlapping phenotype annotations",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Phenotypes.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/Phenotypes.pm",
},
# Draw
{
Expand All @@ -870,7 +870,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"requires_install" => 1,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Draw.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/Draw.pm",
},
# G2P
{
Expand All @@ -880,7 +880,7 @@ my $VEP_PLUGIN_CONFIG = {
"available" => 0,
"enabled" => 0,
"requires_data" => 1,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/G2P.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/G2P.pm",
},

# LocalID
Expand All @@ -890,7 +890,7 @@ 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/94/LocalID.pm",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/95/LocalID.pm",
},


Expand Down

0 comments on commit 663933b

Please sign in to comment.