Codebase list prokka / 782f7572-ec46-411a-af5b-0887825d8872/main
Refresh patches. Debian Janitor 1 year, 6 months ago
2 changed file(s) with 16 addition(s) and 10 deletion(s). Raw diff Collapse all Expand all
+6
-4
debian/patches/hmmer_not_hmmer3 less more
00 Author: Michael R. Crusoe <crusoe@debian.org>
11 Description: Use the Debian binary name for hmmer v3
22 Forwarded: not-needed
3 --- prokka.orig/bin/prokka
4 +++ prokka/bin/prokka
5 @@ -970,7 +970,7 @@
3 Index: prokka.git/bin/prokka
4 ===================================================================
5 --- prokka.git.orig/bin/prokka
6 +++ prokka.git/bin/prokka
7 @@ -970,7 +970,7 @@ unless ($kingdom eq 'Viruses') {
68 push @database, {
79 DB => $dbfile,
810 SRC => "protein motif:$name:",
1113 CMD => $HMMER3CMD,
1214 VERSION => 3, # without this, latest Bioperl goes into infinite loop
1315 }
14 @@ -1013,7 +1013,7 @@
16 @@ -1013,7 +1013,7 @@ if ($hmms) {
1517 unshift @database, {
1618 DB => $hmms,
1719 SRC => $compliant ? "" : "protein motif:$src:",
+10
-6
debian/patches/set-db-dir less more
77
88 ---
99
10 --- prokka.orig/bin/prokka-build_kingdom_dbs
11 +++ prokka/bin/prokka-build_kingdom_dbs
10 Index: prokka.git/bin/prokka-build_kingdom_dbs
11 ===================================================================
12 --- prokka.git.orig/bin/prokka-build_kingdom_dbs
13 +++ prokka.git/bin/prokka-build_kingdom_dbs
1214 @@ -4,7 +4,7 @@
1315 URL="ftp://ftp.ebi.edu.au/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/"
1416
1820
1921 echo "*** NOTICE ***"
2022 echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."
21 @@ -28,7 +28,7 @@
23 @@ -28,7 +28,7 @@ for K in Viruses Archaea Bacteria ; do
2224
2325 wget -q -O - "$DAT" | \
2426 gunzip | \
2729 makeblastdb -in - -dbtype prot -title "Prokka $K" -hash_index -out "$DIR/sprot"
2830
2931 # If you want a copy of the sprot file too (we do for git distribution)
30 --- prokka.orig/bin/prokka
31 +++ prokka/bin/prokka
32 @@ -235,7 +235,7 @@
32 Index: prokka.git/bin/prokka
33 ===================================================================
34 --- prokka.git.orig/bin/prokka
35 +++ prokka.git/bin/prokka
36 @@ -235,7 +235,7 @@ my(@Options, $quiet, $debug, $kingdom, $
3337 $rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
3438 $metagenome, $compliant, $listdb, $citation);
3539