run_get_phylomarkers_pipeline.sh v2.8.0.2_2024-04-14

- snp-sites is called from PATH. Need to compile static version to call via $bindir

run_get_phylomarkers_pipeline.sh

@@ -45,7 +45,7 @@ set -u
 set -o pipefail
 
 progname=${0##*/} # run_get_phylomarkers_pipeline.sh
-VERSION='2.8.0.1_2024-04-14'
+VERSION='2.8.0.2_2024-04-14'
 
 # Set GLOBALS
 # in Strict mode, need to explicitly set undefined variables to an empty string var=''
@@ -1605,7 +1605,7 @@ then
 
 	     # -h doesn't work with globs. Use a for loop
 	     #for i in $(find .. -maxdepth 1 -name "${id}"\* -printf "%f\n")
-	     while read i; do
+	     while read -r i; do
 	         (( DEBUG > 0 )) && msg " > reading top_markers_tab:$top_markers_tab in top_markers_dir:$top_markers_dir; running: ln -s ../${i} ." DEBUG NC
 	         if [ ! -h "$i" ]
 		 then
@@ -2087,11 +2087,13 @@ then
 	    #"${distrodir}"/remove_uninformative_sites_from_aln.pl < concat_cdnAlns.fna > concat_cdnAlns.fnainf
 
 	    # Generate the snp-matrix in FASTA format
-	    "$bindir"/snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna
+	    #"$bindir"/snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna # activate only for statically-linked binary
+	    snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna
 	    check_output concat_cdnAlns_SNPs.fasta "$parent_PID"
 
 	    # Generate the snp-matrix in VCF format
-	    "$bindir"/snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna
+	    #"$bindir"/snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna # activate only for statically-linked binary
+	    snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna
 	    check_output concat_cdnAlns_SNPs.vcf "$parent_PID"
 
 	    # compute phylogeny