removed pgx-main

pgx-main/get_pgx_result_dev.sh

@@ -1,150 +0,0 @@
-#!/bin/bash
-
-bam_s3_bucket="quantgene-wes-archive"
-upload_s3='true'
-download='true'
-index_bam='true'
-dev_suffix="dev_sref_01"
-stellarpgx_ref="stellar_references/cyp2d6_reference_pgx.bed"
-
-declare -A vcf_s3_dict
-declare -A bam_s3_dict
-
-declare -A stellarpgx_ref_dict=(
-  ["sref_00"]="test3.bed"
-  ["sref_01"]="cyp2d6_reference_pgx.bed"
-  ["sref_02"]="cyp2d6_reference_wes_jan6.bed"
-  ["sref_03"]="cyp2d6_reference_wes_march21.bed"
-)
-
-while getopts ':r:nx' 'OPTKEY'; do
-    case ${OPTKEY} in
-        'r')
-            stellarpgx_ref="stellar_references/"${stellarpgx_ref_dict[$OPTARG]}
-            dev_suffix="dev_"$OPTARG
-            ;;
-        'n')
-            download='false'
-            ;;
-        'x')
-            index_bam='false'
-            ;;
-        '?')
-            echo "INVALID OPTION -- ${OPTARG}" >&2
-            exit 1
-            ;;
-        ':')
-            echo "MISSING ARGUMENT for option -- ${OPTARG}" >&2
-            exit 1
-            ;;
-        *)
-            echo "UNIMPLEMENTED OPTION -- ${OPTKEY}" >&2
-            exit 1
-            ;;
-    esac
-done
-
-echo "----------------------------------------------------------------"
-
-# ------------------------ Start PGx Engine --------------------------
-echo -n "Start Docker container: "
-docker start pgx-api
-
-# ------------------------ Empty data folder -------------------------
-if $download; then
-  if ! [ -z "$(ls -A data)" ]; then
-    echo "Remove existing files in data folder"
-    rm -r data/*
-  fi
-fi
-
-# --------------------- Download files from S3 -----------------------
-while IFS= read vcf_s3; do
-  temp=($(echo $vcf_s3 | tr "/" "\n"))
-  vcf_s3_bucket="${temp[1]}"
-  flowcell="${temp[2]}"
-  run="${temp[3]}"
-  sample="${temp[4]::-4}"
-  
-  vcf_s3_prefix="s3://${vcf_s3_bucket}/${flowcell}/${run}"
-  bam_s3_prefix="s3://${bam_s3_bucket}/${run}"
-  
-  vcf_s3_dict[$sample]=$vcf_s3_prefix
-  bam_s3_dict[$sample]=$bam_s3_prefix
-  
-  bam_s3="${bam_s3_prefix}/${sample}.deduped.bam"
-  if $download; then
-    aws s3 cp $vcf_s3 data/
-    aws s3 cp $bam_s3 data/
-    echo "SAMPLE DOWNLOAD COMPlETE"
-  fi
-done
-echo "ALL DOWNLOADS COMPlETE"
-
-# ------------------------ Index BAM files ---------------------------
-if $index_bam; then
-  for f in data/*.bam; do
-    echo "Indexing: "$f
-    samtools index $f $f".bai"
-  done
-fi
-
-# ------------------------ Run Stellar PGx ---------------------------
-echo "Starting stellar PGx"
-cp $stellarpgx_ref resources/cyp2d6/cyp_hg38/test3.bed
-./run_stellar.sh
-
-# ------------------- Generate final PGx Output ----------------------
-for f in data/*.vcf; do
-  s=${f::-4}
-  printf "\nRun PGx Engine for: ${s:5}\n"
-  python3 combine_outside_calls.py $s
-  curl -X 'POST' \
-    'http://localhost:5000/run' \
-    -H 'accept: application/json' \
-    -H 'Content-Type: multipart/form-data' \
-    -F "files=@${s}.vcf;type=text/x-vcard" \
-    -F "files=@${s}_outside_call.tsv" \
-    -o "${s}_pgx_result.zip"
-done
-
-# ----------------------- Stop PGx Engine ----------------------------
-echo ""
-echo -n "Stop Docker container: "
-docker stop pgx-api
-
-
-# ---------------------- Post-Processing -----------------------------
-if ! [ -z "$(ls -A pgx_results)" ]; then
-  echo "Remove existing files in pgx_results folder"
-  rm -r pgx_results/*
-fi
-echo "Copy PGx Output to pgx_results"
-cp data/*.zip pgx_results/
-
-echo "Unzip and create diplotype/rsid overview"
-python3 create_overview.py
-
-echo "Copy over allele files"
-python3 copy_allele_file.py
-
-rm -r work/*
-rm data/*outside*
-rm data/*zip
-rm data/*.alleles
-
-# --------------------- Upload files to S3 ---------------------------
-if $upload_s3; then
-  for result in $(ls -d pgx_results/*); do
-    sample="${result:12:-11}"
-    vcf_s3_prefix=${vcf_s3_dict[$sample]}
-    bam_s3_prefix=${bam_s3_dict[$sample]}
-    aws s3 cp "${result}/output.json" "${vcf_s3_prefix}/${sample}.${dev_suffix}.json" --storage-class INTELLIGENT_TIERING
-    echo -n "Compressing: "
-    tar -zcvf "${result}.${dev_suffix}.tar.gz" "${result}"
-    aws s3 cp "${result}.${dev_suffix}.tar.gz" "${bam_s3_prefix}/" --storage-class INTELLIGENT_TIERING
-  done
-fi
-
-printf "\nDone\n"
-echo "----------------------------------------------------------------"