adding kraken2 scripts to linux binaries

benchmarking/linux-binaries/add_to_library.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# Copyright 2013-2018, Derrick Wood <dwood@cs.jhu.edu>
+#
+# This file is part of the Kraken 2 taxonomic sequence classification system.
+
+# Copy specified file into a Kraken library
+
+set -u  # Protect against uninitialized vars.
+set -e  # Stop on error
+
+LIBRARY_DIR="$KRAKEN2_DB_NAME/library"
+
+if [ ! -e "$1" ]
+then
+  1>&2 echo "Can't add \"$1\": file does not exist"
+  exit 1
+fi
+if [ ! -f "$1" ]
+then
+  1>&2 echo "Can't add \"$1\": not a regular file"
+  exit 1
+fi
+
+add_dir="$LIBRARY_DIR/added"
+mkdir -p "$add_dir"
+prelim_map=$(cp_into_tempfile.pl -t "prelim_map_XXXXXXXXXX" -d "$add_dir" -s txt /dev/null)
+scan_fasta_file.pl "$1" > "$prelim_map"
+
+filename=$(cp_into_tempfile.pl -t "XXXXXXXXXX" -d "$add_dir" -s fna "$1")
+
+if [ -n "$KRAKEN2_MASK_LC" ]; then
+  1>&2 echo -n "Masking low-complexity regions of new file..."
+  mask_low_complexity.sh $filename
+  1>&2 echo " done."
+fi
+
+1>&2 echo "Added \"$1\" to library ($KRAKEN2_DB_NAME)"