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Forwarded: not-needed
Author: Michael R. Crusoe <crusoe@debian.org>
Last-Update: 2020-10-14
Description: Database default path is a user path
not a relative path that would be non FHS compliant
when the prokka script is installed to /usr/bin/
---
--- 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
@@ -235,7 +235,7 @@
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);
-$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
+$dbdir = $ENV{'PROKKA_DBDIR'} || "$ENV{HOME}/.local/lib/prokka/db";
setOptions();
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