[med-svn] r18487 - in trunk/packages: . barrnap barrnap/trunk barrnap/trunk/debian barrnap/trunk/debian/man barrnap/trunk/debian/patches barrnap/trunk/debian/source
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sun Nov 16 22:06:15 UTC 2014
Author: sascha-guest
Date: 2014-11-16 22:06:13 +0000 (Sun, 16 Nov 2014)
New Revision: 18487
Added:
trunk/packages/barrnap/
trunk/packages/barrnap/trunk/
trunk/packages/barrnap/trunk/debian/
trunk/packages/barrnap/trunk/debian/barrnap.install
trunk/packages/barrnap/trunk/debian/barrnap.manpages
trunk/packages/barrnap/trunk/debian/changelog
trunk/packages/barrnap/trunk/debian/compat
trunk/packages/barrnap/trunk/debian/control
trunk/packages/barrnap/trunk/debian/copyright
trunk/packages/barrnap/trunk/debian/docs
trunk/packages/barrnap/trunk/debian/files
trunk/packages/barrnap/trunk/debian/man/
trunk/packages/barrnap/trunk/debian/man/barrnap.1
trunk/packages/barrnap/trunk/debian/patches/
trunk/packages/barrnap/trunk/debian/patches/series
trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs
trunk/packages/barrnap/trunk/debian/rules
trunk/packages/barrnap/trunk/debian/source/
trunk/packages/barrnap/trunk/debian/source/format
trunk/packages/barrnap/trunk/debian/watch
Log:
add first version of barrnap package
Property changes on: trunk/packages/barrnap/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/barrnap/trunk/debian/barrnap.install
===================================================================
--- trunk/packages/barrnap/trunk/debian/barrnap.install (rev 0)
+++ trunk/packages/barrnap/trunk/debian/barrnap.install 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,2 @@
+bin/barrnap usr/bin
+db usr/share/barrnap
Added: trunk/packages/barrnap/trunk/debian/barrnap.manpages
===================================================================
--- trunk/packages/barrnap/trunk/debian/barrnap.manpages (rev 0)
+++ trunk/packages/barrnap/trunk/debian/barrnap.manpages 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+debian/man/*
Added: trunk/packages/barrnap/trunk/debian/changelog
===================================================================
--- trunk/packages/barrnap/trunk/debian/changelog (rev 0)
+++ trunk/packages/barrnap/trunk/debian/changelog 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,5 @@
+barrnap (0.5+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #769641)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 14 Nov 2014 10:12:42 +0000
Added: trunk/packages/barrnap/trunk/debian/compat
===================================================================
--- trunk/packages/barrnap/trunk/debian/compat (rev 0)
+++ trunk/packages/barrnap/trunk/debian/compat 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+9
Added: trunk/packages/barrnap/trunk/debian/control
===================================================================
--- trunk/packages/barrnap/trunk/debian/control (rev 0)
+++ trunk/packages/barrnap/trunk/debian/control 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,23 @@
+Source: barrnap
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1)
+Standards-Version: 3.9.6
+Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/barrnap/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/barrnap/trunk/
+
+Package: barrnap
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
+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
+ (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
+ .
+ It takes FASTA DNA sequence as input, and writes GFF3 as output. It uses the
+ NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.
+ Multithreading is supported and one can expect roughly linear speed-ups
+ with more CPUs.
Added: trunk/packages/barrnap/trunk/debian/copyright
===================================================================
--- trunk/packages/barrnap/trunk/debian/copyright (rev 0)
+++ trunk/packages/barrnap/trunk/debian/copyright 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,24 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: barrnap
+Source: https://github.com/Victorian-Bioinformatics-Consortium/barrnap
+Files-Excluded: binaries/* build/*
+
+Files: *
+Copyright:
+ Copyright 2013 Torsten Seemann <torsten.seemann at monash.edu>
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
Added: trunk/packages/barrnap/trunk/debian/docs
===================================================================
--- trunk/packages/barrnap/trunk/debian/docs (rev 0)
+++ trunk/packages/barrnap/trunk/debian/docs 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+README.md
Added: trunk/packages/barrnap/trunk/debian/files
===================================================================
--- trunk/packages/barrnap/trunk/debian/files (rev 0)
+++ trunk/packages/barrnap/trunk/debian/files 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+barrnap_0.5-1_all.deb science optional
Added: trunk/packages/barrnap/trunk/debian/man/barrnap.1
===================================================================
--- trunk/packages/barrnap/trunk/debian/man/barrnap.1 (rev 0)
+++ trunk/packages/barrnap/trunk/debian/man/barrnap.1 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
+.TH BARRNAP "1" "November 2014" "barrnap 0.4.2" "User Commands"
+.SH NAME
+barrnap \- rapid ribosomal RNA prediction
+.SH SYNOPSIS
+barrnap [options] <chromosomes.fasta>
+.SH DESCRIPTION
+Barrnap predicts the location of ribosomal RNA genes in genomes. It supports
+bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and
+eukaryotes (5S,5.8S,28S,18S).
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+This help
+.TP
+\fB\-\-version\fR
+Print version and exit
+.TP
+\fB\-\-citation\fR
+Print citation for referencing barrnap
+.TP
+\fB\-\-kingdom\fR [X]
+Kingdom: mito bac arc euk (default 'bac')
+.TP
+\fB\-\-quiet\fR
+No screen output (default OFF)
+.TP
+\fB\-\-threads\fR [N]
+Number of threads/cores/CPUs to use (default '8')
+.HP
+\fB\-\-lencutoff\fR [n.n] Proportional length threshold to label as partial (default '0.8')
+.TP
+\fB\-\-reject\fR [n.n]
+Proportional length threshold to reject prediction (default '0.5')
+.TP
+\fB\-\-evalue\fR [n.n]
+Similarity e\-value cut\-off (default '1e\-09')
+.TP
+\fB\-\-incseq\fR
+Include FASTA input sequences in GFF3 output (default OFF)
Added: trunk/packages/barrnap/trunk/debian/patches/series
===================================================================
--- trunk/packages/barrnap/trunk/debian/patches/series (rev 0)
+++ trunk/packages/barrnap/trunk/debian/patches/series 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+use_debian_dirs
Added: trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs
===================================================================
--- trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs (rev 0)
+++ trunk/packages/barrnap/trunk/debian/patches/use_debian_dirs 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,19 @@
+Description: Do not rely on path location relative to barrnap executable
+--- 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 $DBDIR = "$FindBin::RealBin/../db";
++if ( ! -e $DBDIR) {
++ $DBDIR = "/usr/share/barrnap/db";
++}
+ my $OPSYS = $^O;
+ my $NHMMER = "$FindBin::RealBin/../binaries/$OPSYS/nhmmer";
+-
++if ( ! -e $NHMMER ) {
++ $NHMMER = "/usr/bin/nhmmer";
++}
+ my %KINGDOM = (map { substr($_,0,1) => $_ } qw(bac arc euk mito));
+ my %LENG = (
+ "5S_rRNA" =>119, "16S_rRNA"=>1585, "23S_rRNA"=>3232,
Added: trunk/packages/barrnap/trunk/debian/rules
===================================================================
--- trunk/packages/barrnap/trunk/debian/rules (rev 0)
+++ trunk/packages/barrnap/trunk/debian/rules 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+DH_VERBOSE=1
+DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//')
+OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//')
+
+%:
+ dh $@ --parallel
+
+override_dh_auto_build:
+ # pass
+
+override_dh_auto_install:
+ # pass
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz --destdir=..
+ mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz
+
Property changes on: trunk/packages/barrnap/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/barrnap/trunk/debian/source/format
===================================================================
--- trunk/packages/barrnap/trunk/debian/source/format (rev 0)
+++ trunk/packages/barrnap/trunk/debian/source/format 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/barrnap/trunk/debian/watch
===================================================================
--- trunk/packages/barrnap/trunk/debian/watch (rev 0)
+++ trunk/packages/barrnap/trunk/debian/watch 2014-11-16 22:06:13 UTC (rev 18487)
@@ -0,0 +1,4 @@
+version=3
+
+opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/barrnap-$1.tar.gz/,dversionmangle=s/.dfsg// \
+ https://github.com/Victorian-Bioinformatics-Consortium/barrnap/tags .*/v?(\d\S*)\.tar\.gz
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