update ncov_tools to work with results at differing levels within the…

… filesystem

scripts/ncov-tools.py

@@ -255,7 +255,7 @@ def move(cwd, dest, prefix):
 	#print("Don't forget to update the config.yaml file as needed prior to running ncov-tools.")
 	print("Running ncov-tools using %s cores!" %(snakemake.threads))
 
-	subprocess.run([run_script, '-c', str(snakemake.threads), '-s', str(result_dir)])
+	subprocess.run([run_script, '-c', str(snakemake.threads), '-s', str(result_dir), '-n', os.path.join(exec_dir, 'ncov-tools')])
 
 	# clean up
 	shutil.rmtree(data_root)

scripts/run_ncov_tools.sh

@@ -9,6 +9,7 @@ shopt -s extglob
 
 CORES=1
 SIGNAL=0
+NCOV=0
 
 HELP="""
 This script attempts to execute ncov-tools for postprocessing of SIGNAL sequencing data.
@@ -22,10 +23,11 @@ Second argument is '-s' for SIGNAL results directory (namely the name) - much of
 
 """
 
-while getopts ":c:s:" option; do
+while getopts ":c:s:n:" option; do
 	case "${option}" in
 		c) CORES=$OPTARG;; # number of cores
 		s) SIGNAL=$OPTARG;; # SIGNAL results directory
+		n) NCOV=$OPTARG;; # ncov-tools directory
 	esac
 done
 
@@ -40,12 +42,18 @@ if [ $SIGNAL = 0 ] ; then
 	exit 1
 fi
 
+if [ $SIGNAL = 0 ]; then
+	echo "You must specify the path where ncov-tools can be found."
+	echo "$HELP"
+	exit 1
+fi
+
 # Start point for executing from ncov-tools.py is SIGNAL results directory
 RESULTS=$PWD
 
 # determine where ncov-tools is located *add check*
 # change directory to ncov-tools
-cd ../ncov-tools
+cd $NCOV
 
 # run ncov-tools
 snakemake -k -s workflow/Snakefile --cores ${CORES} all

scripts/signal_postprocess.py

@@ -17,7 +17,7 @@
 
 assert long_git_id.startswith('$Id: ')
 #short_git_id = long_git_id[5:12]
-short_git_id = "v1.6.5"
+short_git_id = "v1.6.6"
 
 # Suppresses matplotlib warning (https://github.com/jaleezyy/covid-19-signal/issues/59)
 # Creates a small memory leak, but it's nontrivial to fix, and won't be a practical concern!

signalexe.py

@@ -278,7 +278,7 @@ def install_signal(frontend, data='data', unlock=False):
 	# note: add root_dir to determine the root directory of SIGNAL
 	script_path = os.path.join(os.path.abspath(sys.argv[0]).rsplit("/",1)[0])
 	args, allowed = create_parser()
-	version = 'v1.6.5'
+	version = 'v1.6.6'
 	alt_options = []
 
 	if args.version: