Update gnomad loader to account for massive changes at broad institute

slurm/load_gnomad.slurm

@@ -0,0 +1,61 @@
+#!/bin/bash
+#
+# Project        : PDBMap-gnomAD 
+# Filename       : load_gnomad_gnomad.slurm
+# Author         : R. Michael Sivley, slightly upated by Chris Moth for gnomad v2.1
+# Organization   : Vanderbilt Genetics Institute,
+#                : Department of Biomedical Informatics,
+#                : Vanderbilt University
+# Email          : mike.sivley@vanderbilt.edu
+# Date           : 2015-12-28, updated 2019
+# Description    : Loads gnomAD gnomAD-specific PDBMap. 
+# 
+#
+#=============================================================================#
+# Slurm Parameters
+#SBATCH -J Load_gnomAD
+#SBATCH --mail-user=chris.moth@vanderbilt.edu
+#SBATCH --mail-type=all
+#SBATCH --ntasks=1
+#SBATCH --time=2-6:0:0
+#SBATCH --mem=32GB
+#SBATCH -o ../load_gnomad.slurm.out/load_gnomad.%A[%a].out
+#SBATCH -e ../load_gnomad.slurm.out/load_gnomad.%A[%a].err
+#=============================================================================#
+
+warning="chr1 is the largest load in the slurm array.  MAKE SURE chr1 runs to completion
+The SQL Database can be easily overwhelmed and these processes can exit
+Review tails of all log  and output files"
+
+cd .. # move into pdbmap main directory
+source  /dors/capra_lab/users/mothcw/psbadmin/psb_prep.bash
+# cd - << Directory will not change after all, from above source
+fbase="/dors/capra_lab/data/gnomad/2.1/vcf/exomes/gnomad.exomes.r2.1.sites.chr"
+ftail=".vcf.bgz"
+
+mkdir -pv load_gnomad.slurm.out
+mkdir -pv load_gnomad.slurm.log
+
+if (( ${SLURM_ARRAY_TASK_ID} > 1000000 )); then
+echo "You must start this slurm array script with --array=1-24"
+exit 1
+fi
+
+echo $warning
+
+# Syntax for autosomal chromosomes
+# Launch this script with sbatch --array=1-24 to populate the SLURM_ARRAY_TASK_ID
+chr=${SLURM_ARRAY_TASK_ID}
+
+if (( $chr == 23 )); then
+chr='X'
+elif (( $chr == 24 )); then
+chr='Y'
+fi
+
+
+
+logfile="--logfile=load_gnomad.slurm.log/load_gnomad${chr}.log"
+runcmd="./pdbmap.py ${logfile} load_vcf --novep --noupload --dlabel=gnomad ${fbase}${chr}${ftail}"
+echo "Executing $runcmd"
+`$runcmd`