adds script to set up dependency datasets - #65

.test/setup_dependency_datasets.sh

@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+echo "This script retrieves necessary dataset dependencies for Quac."
+
+PARENT_DIR=$(dirname $(realpath -s $0))
+DATA_DIR="${PARENT_DIR}/dependency_datasets"
+mkdir -p $DATA_DIR && cd $DATA_DIR
+echo "Datasets will be saved in '$DATA_DIR'"
+
+##### retrieve reference genome #####
+echo "setting up reference genome data..."
+REF_GENOME_DIR="${DATA_DIR}/reference_genome"
+mkdir -p $REF_GENOME_DIR && cd $REF_GENOME_DIR
+
+REF_GENOME_FNAME="GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz"
+REF_GENOME_URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/${REF_GENOME_FNAME}
+curl -L $REF_GENOME_URL -o $REF_GENOME_FNAME
+gzip -d $REF_GENOME_FNAME
+
+##### retrieve somalier tool dependencies #####
+echo "setting up somalier dependency datasets..."
+SOMALIER_DIR="${DATA_DIR}/somalier"
+mkdir -p $SOMALIER_DIR && cd $SOMALIER_DIR
+
+curl -L -O "https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz"
+curl -L -O "https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv"
+curl -L -O "https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz"
+tar xzf "1kg.somalier.tar.gz"
+
+##### retrieve VerifyBamID tool dependencies #####
+echo "setting up VerifyBamID dependency datasets..."
+VBID_DIR="${DATA_DIR}/verifyBamID"
+mkdir -p $VBID_DIR && cd $VBID_DIR
+
+VERIFYBAMID_SOURCE_URL="https://raw.githubusercontent.com/Griffan/VerifyBamID/2.0.1"
+
+# genome data
+for FILE_EXT in bed mu UD V; do
+    curl -L -O ${VERIFYBAMID_SOURCE_URL}/resource/1000g.phase3.100k.b38.vcf.gz.dat.${FILE_EXT}
+done
+
+# exome data. Include "chr" prefix to contigs
+mkdir -p exome && cd exome
+curl -L ${VERIFYBAMID_SOURCE_URL}/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat.bed | sed -e 's/^/chr/' - >1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.bed
+curl -L ${VERIFYBAMID_SOURCE_URL}/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat.mu | sed -e 's/^/chr/' - >1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.mu
+curl -L ${VERIFYBAMID_SOURCE_URL}/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat.UD >1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.UD
+curl -L ${VERIFYBAMID_SOURCE_URL}/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat.V >1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.V