diff --git a/plugin_config.txt b/plugin_config.txt index 75687c62..45d80088 100644 --- a/plugin_config.txt +++ b/plugin_config.txt @@ -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" => [ @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" => [ @@ -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" @@ -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" @@ -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", }, @@ -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 @@ -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" => [ "@*" ], @@ -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" ] }, @@ -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", }, @@ -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" => [ @@ -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", }, @@ -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 @@ -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" => [ "@*" @@ -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 @@ -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", }, @@ -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", }, @@ -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 @@ -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 @@ -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 @@ -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 { @@ -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 { @@ -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 @@ -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", },