IGV S3 to HTTP bridge

igv_regenerate.sh

#!/bin/bash
##### CONFIG
S3FUSE_MNT=/mnt/igv
IGV_NGINX_MNT=/var/www/igv
IGV_XML_HEAD="<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<Global name=\"UMCCR AWS IGV server\" version=\"1\">\n<Category name=\"UMCCR Amazon IGV bucket\">"
IGV_XML_BODY_TMPL="<Resource name=\"SAMPLE\" path=\"URL\"></Resource>\n"
IGV_XML_TAIL="</Category>\n</Global>\n"

IGV_XML_BODY_ARRAY=()

IGV_URL_PREFIX="https://igv.dev.umccr.org/igv/"
IGV_XML_REGISTRY_FILE="umccr_registry.xml"
#####


for sample_path in `find $S3FUSE_MNT \( -iname "*.vcf.gz" -o -iname "*.bam" \)`
do
    # Creates symlinks from S3 to NGINX
    IGV_MNT=$IGV_NGINX_MNT/`basename "$sample_path"`
    SAMPLENAME=`basename $sample_path`

    if [[ $sample_path == *".bam"* ]]; then
	ln -sf $sample_path $IGV_MNT
	ln -sf $sample_path.bai $IGV_MNT.bai
    elif [[ $sample_path == *".vcf.gz" ]]; then
	ln -sf $sample_path $IGV_MNT
	ln -sf $sample_path.tbi $IGV_MNT.tbi
    fi

    # Builds XML body spec (see IGV XML FILE generation below)
    IGV_XML_BODY="${IGV_XML_BODY_TMPL/SAMPLE/$SAMPLENAME}"
    IGV_XML_BODY="${IGV_XML_BODY/URL/${IGV_URL_PREFIX}${SAMPLENAME}}"

    IGV_XML_BODY_ARRAY+="$IGV_XML_BODY"
done

# Generates IGV XML FILE
echo -e "$IGV_XML_HEAD" > "$IGV_XML_REGISTRY_FILE"
for sample_url in "$IGV_XML_BODY_ARRAY"
do
   echo -e "$sample_url" >> "$IGV_XML_REGISTRY_FILE"
done
echo -e "$IGV_XML_TAIL" >> "$IGV_XML_REGISTRY_FILE"