Description: Use a FHS path to the databases, not a relative path that would
 be non FHS compliant when the prokka script is installed to /usr/bin/
Forwarded: not-needed
Author: Michael R. Crusoe <mcrusoe@msu.edu>
Last-Update: 2015-02-21

---

--- prokka.orig/bin/prokka-build_kingdom_dbs
+++ prokka/bin/prokka-build_kingdom_dbs
@@ -4,7 +4,7 @@
 URL="ftp://ftp.ebi.edu.au/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/"
 
 # where to put formatted database: /path/to/prokka/db/
-ROOTDIR=$(dirname $0)
+ROOTDIR=/var/lib/prokka/db
 
 echo "*** NOTICE ***"
 echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."
@@ -28,7 +28,7 @@
 
   wget -q -O - "$DAT" | \
     gunzip | \
-    "$ROOTDIR/prokka-uniprot_to_fasta_db" | \
+    prokka-uniprot_to_fasta_db | \
     makeblastdb -in - -dbtype prot -title "Prokka $K" -hash_index -out "$DIR/sprot"
 
   # If you want a copy of the sprot file too (we do for git distribution)
--- prokka.orig/bin/prokka
+++ prokka/bin/prokka
@@ -232,7 +232,7 @@
              $rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
 	     $metagenome, $compliant, $listdb, $citation);
 
-$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
+$dbdir = $ENV{'PROKKA_DBDIR'} || "/var/lib/prokka/db";
 
 setOptions();
 
