[med-svn] r19765 - in trunk/packages/barrnap/trunk/debian: . patches

[Sascha Steinbiss]

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 <sascha at 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.seemann at monash.edu>';
- my $URL = 'http://www.vicbioinformatics.com/';
+ my $AUTHOR = 'Torsten Seemann <torsten.seemann at gmail.com>';
+ my $URL = 'https://github.com/Victorian-Bioinformatics-Consortium/barrnap';
  my $DBDIR = "$FindBin::RealBin/../db";
 +if ( ! -e $DBDIR) {
 +  $DBDIR = "/usr/share/barrnap/db";