Author: sascha-guest
Date: 2015-07-29 18:17:03 +0000 (Wed, 29 Jul 2015)
New Revision: 19765
Modified:
trunk/packages/barrnap/trunk/debian/changelog
trunk/packages/barrnap/trunk/debian/control
trunk/packages/barrnap/trunk/debian/patches/use_both_hmmsets
trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs
Log:
new upstream release
Modified: trunk/packages/barrnap/trunk/debian/changelog
===================================================================
--- trunk/packages/barrnap/trunk/debian/changelog 2015-07-29 17:59:24 UTC
(rev 19764)
+++ trunk/packages/barrnap/trunk/debian/changelog 2015-07-29 18:17:03 UTC
(rev 19765)
@@ -1,3 +1,10 @@
+barrnap (0.7+dfsg-1) unstable; urgency=low
+
+ * New upstream release.
+ * Remove Suggests: to non-existent barrnap=data-nonfree package
+
+ -- Sascha Steinbiss <sas...@steinbiss.name> Wed, 29 Jul 2015 18:05:14 +0000
+
barrnap (0.5+dfsg-1) unstable; urgency=low
* Initial release (Closes: #769641)
Modified: trunk/packages/barrnap/trunk/debian/control
===================================================================
--- trunk/packages/barrnap/trunk/debian/control 2015-07-29 17:59:24 UTC (rev
19764)
+++ trunk/packages/barrnap/trunk/debian/control 2015-07-29 18:17:03 UTC (rev
19765)
@@ -12,7 +12,6 @@
Package: barrnap
Architecture: all
Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
-Suggests: barrnap-data-nonfree
Description: rapid ribosomal RNA prediction
Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
Modified: trunk/packages/barrnap/trunk/debian/patches/use_both_hmmsets
===================================================================
--- trunk/packages/barrnap/trunk/debian/patches/use_both_hmmsets
2015-07-29 17:59:24 UTC (rev 19764)
+++ trunk/packages/barrnap/trunk/debian/patches/use_both_hmmsets
2015-07-29 18:17:03 UTC (rev 19765)
@@ -70,7 +70,7 @@
foreach (@hits) {
chomp;
err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i;
-@@ -102,7 +118,7 @@
+@@ -103,7 +119,7 @@
# check for incomplete alignments
my $note = '';
my $len = $end-$begin+1;
@@ -79,7 +79,7 @@
if ( $len < int($reject * $LENG{$gene}) ) {
msg("Rejecting short $len nt predicted $gene. Adjust via --reject
option.");
next HIT;
-@@ -120,7 +136,7 @@
+@@ -121,7 +137,7 @@
];
}
@@ -88,7 +88,7 @@
# output a sorted GFF3
sub gff_sort {
-@@ -168,13 +184,13 @@
+@@ -169,13 +185,13 @@
sub show_citation {
print STDERR << "EOCITE";
@@ -104,7 +104,7 @@
Thank you.
EOCITE
-@@ -193,7 +209,7 @@
+@@ -194,7 +210,7 @@
{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
{OPT=>"version", VAR=>\&version, DESC=>"Print version and
exit"},
{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for
referencing $EXE"},
@@ -113,7 +113,7 @@
DESC=>"Kingdom: ".join(' ', values %KINGDOM) },
{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
{OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of
threads/cores/CPUs to use"},
-@@ -226,15 +242,15 @@
+@@ -227,15 +243,15 @@
my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
$def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
my $opt = $_->{OPT};
Modified: trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs
===================================================================
--- trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs 2015-07-29
17:59:24 UTC (rev 19764)
+++ trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs 2015-07-29
18:17:03 UTC (rev 19765)
@@ -2,8 +2,8 @@
--- a/bin/barrnap
+++ b/bin/barrnap
@@ -14,9 +14,14 @@
- my $AUTHOR = 'Torsten Seemann <torsten.seem...@monash.edu>';
- my $URL = 'http://www.vicbioinformatics.com/';
+ my $AUTHOR = 'Torsten Seemann <torsten.seem...@gmail.com>';
+ my $URL = 'https://github.com/Victorian-Bioinformatics-Consortium/barrnap';
my $DBDIR = "$FindBin::RealBin/../db";
+if ( ! -e $DBDIR) {
+ $DBDIR = "/usr/share/barrnap/db";
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