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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
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run_get_phylomarkers_pipeline.sh

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

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