added a stage-in script to ensure minimal amount of communication (e.g. ssh) for stage-in

blast/parallel_BLAST/stage_in.sh

+
+function stage_in_writer() {
+cat <<EOF > $stagefile
+#!/bin/bash
+target=/localscratch/$SLURM_JOB_ID/ramdisk
+cd \$target
+for fname in \$(find ${DATABASEPATH} -type f ); do
+    suffix=\${fname#*.}
+    outfile=db.\${suffix}
+    dd bs=4048 if=\$fname of=\$outfile &
+done
+cd -
+EOF
+}
+
+