Package list barrnap / 21fd0fe
add first version of barrnap package Sascha Steinbiss 6 years ago
14 changed file(s) with 144 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
0 bin/barrnap usr/bin
1 db usr/share/barrnap
0 barrnap (0.5+dfsg-1) UNRELEASED; urgency=low
1
2 * Initial release (Closes: #769641)
3
4 -- Sascha Steinbiss <sascha@steinbiss.name> Fri, 14 Nov 2014 10:12:42 +0000
0 Source: barrnap
1 Section: science
2 Priority: optional
3 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
4 Uploaders: Sascha Steinbiss <sascha@steinbiss.name>
5 Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1)
6 Standards-Version: 3.9.6
7 Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml
8 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/barrnap/trunk/
9 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/barrnap/trunk/
10
11 Package: barrnap
12 Architecture: all
13 Depends: ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
14 Description: rapid ribosomal RNA prediction
15 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
16 ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
17 (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
18 .
19 It takes FASTA DNA sequence as input, and writes GFF3 as output. It uses the
20 NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.
21 Multithreading is supported and one can expect roughly linear speed-ups
22 with more CPUs.
0 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
1 Upstream-Name: barrnap
2 Source: https://github.com/Victorian-Bioinformatics-Consortium/barrnap
3 Files-Excluded: binaries/* build/*
4
5 Files: *
6 Copyright:
7 Copyright 2013 Torsten Seemann <torsten.seemann@monash.edu>
8 License: GPL-3+
9 This program is free software: you can redistribute it and/or modify
10 it under the terms of the GNU General Public License as published by
11 the Free Software Foundation, either version 3 of the License, or
12 (at your option) any later version.
13 .
14 This package is distributed in the hope that it will be useful,
15 but WITHOUT ANY WARRANTY; without even the implied warranty of
16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 GNU General Public License for more details.
18 .
19 You should have received a copy of the GNU General Public License
20 along with this program. If not, see <http://www.gnu.org/licenses/>.
21 .
22 On Debian systems, the complete text of the GNU General
23 Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
0 README.md
0 barrnap_0.5-1_all.deb science optional
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
1 .TH BARRNAP "1" "November 2014" "barrnap 0.4.2" "User Commands"
2 .SH NAME
3 barrnap \- rapid ribosomal RNA prediction
4 .SH SYNOPSIS
5 barrnap [options] <chromosomes.fasta>
6 .SH DESCRIPTION
7 Barrnap predicts the location of ribosomal RNA genes in genomes. It supports
8 bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and
9 eukaryotes (5S,5.8S,28S,18S).
10 .SH OPTIONS
11 .TP
12 \fB\-\-help\fR
13 This help
14 .TP
15 \fB\-\-version\fR
16 Print version and exit
17 .TP
18 \fB\-\-citation\fR
19 Print citation for referencing barrnap
20 .TP
21 \fB\-\-kingdom\fR [X]
22 Kingdom: mito bac arc euk (default 'bac')
23 .TP
24 \fB\-\-quiet\fR
25 No screen output (default OFF)
26 .TP
27 \fB\-\-threads\fR [N]
28 Number of threads/cores/CPUs to use (default '8')
29 .HP
30 \fB\-\-lencutoff\fR [n.n] Proportional length threshold to label as partial (default '0.8')
31 .TP
32 \fB\-\-reject\fR [n.n]
33 Proportional length threshold to reject prediction (default '0.5')
34 .TP
35 \fB\-\-evalue\fR [n.n]
36 Similarity e\-value cut\-off (default '1e\-09')
37 .TP
38 \fB\-\-incseq\fR
39 Include FASTA input sequences in GFF3 output (default OFF)
0 use_debian_dirs
0 Description: Do not rely on path location relative to barrnap executable
1 --- a/bin/barrnap
2 +++ b/bin/barrnap
3 @@ -14,9 +14,14 @@
4 my $AUTHOR = 'Torsten Seemann <torsten.seemann@monash.edu>';
5 my $URL = 'http://www.vicbioinformatics.com/';
6 my $DBDIR = "$FindBin::RealBin/../db";
7 +if ( ! -e $DBDIR) {
8 + $DBDIR = "/usr/share/barrnap/db";
9 +}
10 my $OPSYS = $^O;
11 my $NHMMER = "$FindBin::RealBin/../binaries/$OPSYS/nhmmer";
12 -
13 +if ( ! -e $NHMMER ) {
14 + $NHMMER = "/usr/bin/nhmmer";
15 +}
16 my %KINGDOM = (map { substr($_,0,1) => $_ } qw(bac arc euk mito));
17 my %LENG = (
18 "5S_rRNA" =>119, "16S_rRNA"=>1585, "23S_rRNA"=>3232,
0 #!/usr/bin/make -f
1 # -*- makefile -*-
2
3 DH_VERBOSE=1
4 DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
5 VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//')
6 OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//')
7
8 %:
9 dh $@ --parallel
10
11 override_dh_auto_build:
12 # pass
13
14 override_dh_auto_install:
15 # pass
16
17 get-orig-source:
18 uscan --verbose --force-download --repack --compression xz --destdir=..
19 mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz
20
0 3.0 (quilt)
0 version=3
1
2 opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/barrnap-$1.tar.gz/,dversionmangle=s/.dfsg// \
3 https://github.com/Victorian-Bioinformatics-Consortium/barrnap/tags .*/v?(\d\S*)\.tar\.gz