new upstream release
Sascha Steinbiss
8 years ago
|
0 |
barrnap (0.7+dfsg-1) unstable; urgency=low
|
|
1 |
|
|
2 |
* New upstream release.
|
|
3 |
* Remove Suggests: to non-existent barrnap=data-nonfree package
|
|
4 |
|
|
5 |
-- Sascha Steinbiss <sascha@steinbiss.name> Wed, 29 Jul 2015 18:05:14 +0000
|
|
6 |
|
| 0 | 7 |
barrnap (0.5+dfsg-1) unstable; urgency=low
|
| 1 | 8 |
|
| 2 | 9 |
* Initial release (Closes: #769641)
|
| 11 | 11 |
Package: barrnap
|
| 12 | 12 |
Architecture: all
|
| 13 | 13 |
Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
|
| 14 | |
Suggests: barrnap-data-nonfree
|
| 15 | 14 |
Description: rapid ribosomal RNA prediction
|
| 16 | 15 |
Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
|
| 17 | 16 |
ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
|
| 69 | 69 |
foreach (@hits) {
|
| 70 | 70 |
chomp;
|
| 71 | 71 |
err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i;
|
| 72 | |
@@ -102,7 +118,7 @@
|
|
72 |
@@ -103,7 +119,7 @@
|
| 73 | 73 |
# check for incomplete alignments
|
| 74 | 74 |
my $note = '';
|
| 75 | 75 |
my $len = $end-$begin+1;
|
|
| 78 | 78 |
if ( $len < int($reject * $LENG{$gene}) ) {
|
| 79 | 79 |
msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
|
| 80 | 80 |
next HIT;
|
| 81 | |
@@ -120,7 +136,7 @@
|
|
81 |
@@ -121,7 +137,7 @@
|
| 82 | 82 |
];
|
| 83 | 83 |
}
|
| 84 | 84 |
|
|
| 87 | 87 |
# output a sorted GFF3
|
| 88 | 88 |
|
| 89 | 89 |
sub gff_sort {
|
| 90 | |
@@ -168,13 +184,13 @@
|
|
90 |
@@ -169,13 +185,13 @@
|
| 91 | 91 |
|
| 92 | 92 |
sub show_citation {
|
| 93 | 93 |
print STDERR << "EOCITE";
|
|
| 103 | 103 |
Thank you.
|
| 104 | 104 |
|
| 105 | 105 |
EOCITE
|
| 106 | |
@@ -193,7 +209,7 @@
|
|
106 |
@@ -194,7 +210,7 @@
|
| 107 | 107 |
{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
|
| 108 | 108 |
{OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"},
|
| 109 | 109 |
{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing $EXE"},
|
|
| 112 | 112 |
DESC=>"Kingdom: ".join(' ', values %KINGDOM) },
|
| 113 | 113 |
{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
|
| 114 | 114 |
{OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of threads/cores/CPUs to use"},
|
| 115 | |
@@ -226,15 +242,15 @@
|
|
115 |
@@ -227,15 +243,15 @@
|
| 116 | 116 |
my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
|
| 117 | 117 |
$def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
|
| 118 | 118 |
my $opt = $_->{OPT};
|
| 1 | 1 |
--- a/bin/barrnap
|
| 2 | 2 |
+++ b/bin/barrnap
|
| 3 | 3 |
@@ -14,9 +14,14 @@
|
| 4 | |
my $AUTHOR = 'Torsten Seemann <torsten.seemann@monash.edu>';
|
| 5 | |
my $URL = 'http://www.vicbioinformatics.com/';
|
|
4 |
my $AUTHOR = 'Torsten Seemann <torsten.seemann@gmail.com>';
|
|
5 |
my $URL = 'https://github.com/Victorian-Bioinformatics-Consortium/barrnap';
|
| 6 | 6 |
my $DBDIR = "$FindBin::RealBin/../db";
|
| 7 | 7 |
+if ( ! -e $DBDIR) {
|
| 8 | 8 |
+ $DBDIR = "/usr/share/barrnap/db";
|