From a39bb49de391a6a862c03be19e52f4be3937b6d1 Mon Sep 17 00:00:00 2001
From: jkgoodrich <jgoodric@broadinstitute.org>
Date: Wed, 8 Sep 2021 14:57:40 -0600
Subject: [PATCH] Add VEP 101 init

---
 init_scripts/vep101-init.sh | 100 ++++++++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 init_scripts/vep101-init.sh

diff --git a/init_scripts/vep101-init.sh b/init_scripts/vep101-init.sh
new file mode 100644
index 000000000..6bf8b3177
--- /dev/null
+++ b/init_scripts/vep101-init.sh
@@ -0,0 +1,100 @@
+#!/bin/bash
+
+export PROJECT="$(gcloud config get-value project)"
+export VEP_CONFIG_PATH="$(/usr/share/google/get_metadata_value attributes/VEP_CONFIG_PATH)"
+export VEP_REPLICATE="$(/usr/share/google/get_metadata_value attributes/VEP_REPLICATE)"
+export VEP_BUCKET=hail-${VEP_REPLICATE}-vep
+export ASSEMBLY=GRCh38
+export VEP_DOCKER_IMAGE=gcr.io/broad-mpg-gnomad/vep_101
+
+mkdir -p /vep_data/loftee_data
+mkdir -p /vep_data/homo_sapiens
+
+# Install docker
+apt-get update
+apt-get -y install \
+    apt-transport-https \
+    ca-certificates \
+    curl \
+    gnupg2 \
+    software-properties-common \
+    tabix
+curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add -
+sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable"
+apt-get update
+apt-get install -y --allow-unauthenticated docker-ce
+
+
+gsutil -u $PROJECT cat gs://${VEP_BUCKET}/loftee-beta/${ASSEMBLY}.tar | tar -xf - -C /vep_data/ &
+gsutil -u $PROJECT cat gs://${VEP_BUCKET}/Plugins.tar /vep_data/Plugins.tar | tar -xf - -C /vep_data
+docker pull ${VEP_DOCKER_IMAGE} &
+wait
+
+################################################################
+# Added stuff
+################################################################
+
+# GCS copy of ftp://ftp.ensembl.org/pub/release-101/variation/indexed_vep_cache/homo_sapiens_merged_vep_101_GRCh38.tar.gz
+gsutil -u $PROJECT cat gs://gnomad-public-requester-pays/resources/vep/v101/homo_sapiens_merged_vep_101_GRCh38.tar.gz | tar -xzf - -C /vep_data
+
+wait
+
+# FASTA file from Hail's VEP 101 data
+gsutil -u $PROJECT cp gs://gnomad-public-requester-pays/resources/vep/Homo_sapiens.GRCh38.dna.toplevel.fa.gz /vep_data/
+gsutil -u $PROJECT cp gs://gnomad-public-requester-pays/resources/vep/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai /vep_data/
+gsutil -u $PROJECT cp gs://gnomad-public-requester-pays/resources/vep/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.gzi /vep_data/
+
+# Create config file.
+
+cat > /vep_data/vep101-GRCh38.json <<EOF
+{"command": [
+    "/vep",
+    "--format", "vcf",
+    "__OUTPUT_FORMAT_FLAG__",
+    "--everything",
+    "--allele_number",
+    "--no_stats",
+    "--cache", "--offline",
+    "--minimal",
+    "--assembly", "GRCh38",
+    "--merged",
+    "--fasta", "/opt/vep/.vep/Homo_sapiens.GRCh38.dna.toplevel.fa.gz",
+    "--plugin", "LoF,loftee_path:/opt/vep/Plugins/,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql",
+    "--dir_plugins", "/opt/vep/Plugins/",
+    "-o", "STDOUT"
+],
+ "env": {},
+ "vep_json_schema": "Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,tsl:Int32,uniparc:String,variant_allele:String}],variant_class:String}"
+}
+EOF
+
+ln -s /vep_data/vep101-GRCh38.json $VEP_CONFIG_PATH
+
+
+################################################################
+# End added stuff
+################################################################
+
+cat >/vep.c <<EOF
+#include <unistd.h>
+#include <stdio.h>
+
+int
+main(int argc, char *const argv[]) {
+  if (setuid(geteuid()))
+    perror( "setuid" );
+
+  execv("/vep.sh", argv);
+  return 0;
+}
+EOF
+gcc -Wall -Werror -O2 /vep.c -o /vep
+chmod u+s /vep
+
+cat >/vep.sh <<EOF
+#!/bin/bash
+
+docker run -i -v /vep_data/:/opt/vep/.vep/:ro ${VEP_DOCKER_IMAGE} \
+  /opt/vep/src/ensembl-vep/vep "\$@"
+EOF
+chmod +x /vep.sh