[med-svn] r12975 - in trunk/packages: . aragorn aragorn/trunk aragorn/trunk/debian aragorn/trunk/debian/man aragorn/trunk/debian/patches aragorn/trunk/debian/source
Sascha Steinbiss
sascha-guest at alioth.debian.org
Sun Feb 10 14:54:53 UTC 2013
Author: sascha-guest
Date: 2013-02-10 14:54:53 +0000 (Sun, 10 Feb 2013)
New Revision: 12975
Added:
trunk/packages/aragorn/
trunk/packages/aragorn/trunk/
trunk/packages/aragorn/trunk/debian/
trunk/packages/aragorn/trunk/debian/aragorn.install
trunk/packages/aragorn/trunk/debian/aragorn.manpages
trunk/packages/aragorn/trunk/debian/changelog
trunk/packages/aragorn/trunk/debian/compat
trunk/packages/aragorn/trunk/debian/control
trunk/packages/aragorn/trunk/debian/copyright
trunk/packages/aragorn/trunk/debian/get-orig-source
trunk/packages/aragorn/trunk/debian/man/
trunk/packages/aragorn/trunk/debian/man/aragorn.1
trunk/packages/aragorn/trunk/debian/manpage.1.src
trunk/packages/aragorn/trunk/debian/patches/
trunk/packages/aragorn/trunk/debian/patches/formatstrings
trunk/packages/aragorn/trunk/debian/patches/hardening
trunk/packages/aragorn/trunk/debian/patches/series
trunk/packages/aragorn/trunk/debian/rules
trunk/packages/aragorn/trunk/debian/source/
trunk/packages/aragorn/trunk/debian/source/format
trunk/packages/aragorn/trunk/debian/upstream
trunk/packages/aragorn/trunk/debian/watch
Log:
add aragorn draft
Property changes on: trunk/packages/aragorn/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/aragorn/trunk/debian/aragorn.install
===================================================================
--- trunk/packages/aragorn/trunk/debian/aragorn.install (rev 0)
+++ trunk/packages/aragorn/trunk/debian/aragorn.install 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,2 @@
+usr/bin/aragorn
+usr/bin/aragorn
Added: trunk/packages/aragorn/trunk/debian/aragorn.manpages
===================================================================
--- trunk/packages/aragorn/trunk/debian/aragorn.manpages (rev 0)
+++ trunk/packages/aragorn/trunk/debian/aragorn.manpages 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1 @@
+debian/man/*
Added: trunk/packages/aragorn/trunk/debian/changelog
===================================================================
--- trunk/packages/aragorn/trunk/debian/changelog (rev 0)
+++ trunk/packages/aragorn/trunk/debian/changelog 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,5 @@
+aragorn (1.2.34-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 06 Feb 2013 10:02:30 +0100
Added: trunk/packages/aragorn/trunk/debian/compat
===================================================================
--- trunk/packages/aragorn/trunk/debian/compat (rev 0)
+++ trunk/packages/aragorn/trunk/debian/compat 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1 @@
+9
Added: trunk/packages/aragorn/trunk/debian/control
===================================================================
--- trunk/packages/aragorn/trunk/debian/control (rev 0)
+++ trunk/packages/aragorn/trunk/debian/control 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,19 @@
+Source: aragorn
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
+Build-Depends: debhelper (>= 9), hardening-includes
+Standards-Version: 3.9.4
+Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
+Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/aragorn/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/aragorn/trunk/
+
+Package: aragorn
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: tRNA and tmRNA detection in nucleotide sequences
+ The program employs heuristic algorithms to predict tRNA secondary structure,
+ based on homology with recognized tRNA consensus sequences and ability to form
+ a base-paired cloverleaf. tmRNA genes are identified using a modified version
+ of the BRUCE program.
Added: trunk/packages/aragorn/trunk/debian/copyright
===================================================================
--- trunk/packages/aragorn/trunk/debian/copyright (rev 0)
+++ trunk/packages/aragorn/trunk/debian/copyright 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,22 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: aragorn
+Source: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
+
+Files: *
+Copyright: Copyright: 2003-2015 Dean Laslett <gaiaquark at gmail.com>
+License: GPL-2+
+ This package 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 2 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 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/aragorn/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/aragorn/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/aragorn/trunk/debian/get-orig-source 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,41 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+COMPRESS=gz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+rm -rf *
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+mkdir ${TARDIR}
+cp ../${NAME}${VERSION}.c ${TARDIR}
+rm -f ../${NAME}${VERSION}.c
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
+cd ..
+cp tarballs/${NAME}_${VERSION}.orig.tar.gz .
Property changes on: trunk/packages/aragorn/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/aragorn/trunk/debian/man/aragorn.1
===================================================================
--- trunk/packages/aragorn/trunk/debian/man/aragorn.1 (rev 0)
+++ trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,169 @@
+'\" t
+.\" Title: aragorn
+.\" Author: [see the "AUTHORS" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 02/09/2013
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "ARAGORN" "1" "02/09/2013" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+aragorn \- detect tRNA genes in nucleotide sequences
+.SH "SYNOPSIS"
+.sp
+\fBaragorn\fR \-v \-s \-d \-c \-l \-j \-a \-q \-rn \-w \-ifro<min>,<max> \-t \-m \-mt \-gc \-tv \-seq \-br \-fasta \-fo \-o <outfile> <filename>
+.SH "OPTIONS"
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+\-m Search for tmRNA genes\&.
+\-t Search for tRNA genes\&.
+ By default, all are detected\&. If one of
+ \-m or \-t is specified, then the other
+ is not detected unless specified as well\&.
+\-mt Search for Metazoan mitochondrial tRNA genes\&.
+ tRNA genes with introns not detected\&. \-i,\-sr switchs
+ ignored\&. Composite Metazoan mitochondrial
+ genetic code used\&.
+\-mtmam Search for Mammalian mitochondrial tRNA
+ genes\&. \-i,\-sr switchs ignored\&. \-tv switch set\&.
+ Mammalian mitochondrial genetic code used\&.
+\-mtx Same as \-mt but low scoring tRNA genes are
+ not reported\&.
+\-mtd Overlapping metazoan mitochondrial tRNA genes
+ on opposite strands are reported\&.
+\-gc<num> Use the GenBank transl_table = <num> genetic code\&.
+\-gcstd Use standard genetic code\&.
+\-gcmet Use composite Metazoan mitochondrial genetic code\&.
+\-gcvert Use Vertebrate mitochondrial genetic code\&.
+\-gcinvert Use Invertebrate mitochondrial genetic code\&.
+\-gcyeast Use Yeast mitochondrial genetic code\&.
+\-gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code\&.
+\-gcciliate Use Ciliate genetic code\&.
+\-gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code
+\-gceuplot Use Euplotid genetic code\&.
+\-gcbact Use Bacterial/Plant Chloroplast genetic code\&.
+\-gcaltyeast Use alternative Yeast genetic code\&.
+\-gcascid Use Ascidian Mitochondrial genetic code\&.
+\-gcaltflat Use alternative Flatworm Mitochondrial genetic code\&.
+\-gcblep Use Blepharisma genetic code\&.
+\-gcchloroph Use Chlorophycean Mitochondrial genetic code\&.
+\-gctrem Use Trematode Mitochondrial genetic code\&.
+\-gcscen Use Scenedesmus obliquus Mitochondrial genetic code\&.
+\-gcthraust Use Thraustochytrium Mitochondrial genetic code\&.
+ Individual modifications can be appended using
+,BBB=<aa> B = A,C,G, or T\&. <aa> is the three letter
+ code for an amino\-acid\&. More than one modification
+ can be specified\&. eg \-gcvert,aga=Trp,agg=Trp uses
+ the Vertebrate Mitochondrial code and the codons
+ AGA and AGG changed to Tryptophan\&.
+\-tv Do not search for mitochondrial TV replacement
+ loop tRNA genes\&. Only relevant if \-mt used\&.
+\-c7 Search for tRNA genes with 7 base C\-loops only\&.
+\-i Search for tRNA genes with introns in
+ anticodon loop with maximum length 3000
+ bases\&. Minimum intron length is 0 bases\&.
+ Ignored if \-m is specified\&.
+\-i<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases\&. Minimum intron length is 0 bases\&.
+ Ignored if \-m is specified\&.
+\-i<min>,<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases, and minimum length <min> bases\&.
+ Ignored if \-m is specified\&.
+\-io Same as \-i, but allow tRNA genes with long
+ introns to overlap shorter tRNA genes\&.
+\-if Same as \-i, but fix intron between positions
+ 37 and 38 on C\-loop (one base after anticodon)\&.
+\-ifo Same as \-if and \-io combined\&.
+\-ir Same as \-i, but report tRNA genes with minimum
+ length <min> bases rather than search for
+ tRNA genes with minimum length <min> bases\&.
+ With this switch, <min> acts as an output filter,
+ minimum intron length for searching is still 0 bases\&.
+\-c Assume that each sequence has a circular
+ topology\&. Search wraps around each end\&.
+ Default setting\&.
+\-l Assume that each sequence has a linear
+ topology\&. Search does not wrap\&.
+\-d Double\&. Search both strands of each
+ sequence\&. Default setting\&.
+\-s or \-s+ Single\&. Do not search the complementary
+ (antisense) strand of each sequence\&.
+\-sc or \-s\- Single complementary\&. Do not search the sense
+ strand of each sequence\&.
+\-ps Lower scoring thresholds to 95% of default levels\&.
+\-ps<num> Change scoring thresholds to <num> percent of default levels\&.
+\-rp Report possible pseudogenes (normalised score < 100)\&.
+\-seq Print out primary sequence\&.
+\-br Show secondary structure of tRNA gene primary sequence
+ using round brackets\&.
+\-fasta Print out primary sequence in fasta format\&.
+\-fo Print out primary sequence in fasta format only
+ (no secondary structure)\&.
+\-fon Same as \-fo, with sequence and gene numbering in header\&.
+\-fos Same as \-fo, with no spaces in header\&.
+\-fons Same as \-fo, with sequence and gene numbering, but no spaces\&.
+\-w Print out in Batch mode\&.
+\-ss Use the stricter canonical 1\-2 bp spacer1 and
+ 1 bp spacer2\&. Ignored if \-mt set\&. Default is to
+ allow 3 bp spacer1 and 0\-2 bp spacer2, which may
+ degrade selectivity\&.\en");
+\-v Verbose\&. Prints out information during
+ search to STDERR\&.
+\-a Print out tRNA domain for tmRNA genes\&.
+\-a7 Restrict tRNA astem length to a maximum of 7 bases
+\-aa Display message if predicted iso\-acceptor species
+ does not match species in sequence name (if present)\&.
+\-j Display 4\-base sequence on 3\*(Aq end of astem
+ regardless of predicted amino\-acyl acceptor length\&.
+\-jr Allow some divergence of 3\*(Aq amino\-acyl acceptor
+ sequence from NCCA\&.
+\-jr4 Allow some divergence of 3\*(Aq amino\-acyl acceptor
+ sequence from NCCA, and display 4 bases\&.
+\-q Dont print configuration line (which switchs
+ and files were used)\&.
+\-rn Repeat sequence name before summary information\&.
+\-O <outfile> Print output to <outfile>\&. If <outfile>
+ already exists, it is overwritten\&. By default
+ all output goes to stdout\&.
+.fi
+.if n \{\
+.RE
+.\}
+.SH "DESCRIPTION"
+.sp
+aragorn detects tRNA, mtRNA, and tmRNA genes\&. A minimum requirement is at least a 32 bit compiler architecture (variable types int and unsigned int are at least 4 bytes long)\&.
+.sp
+<filename> is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&.
+.SH "AUTHORS"
+.sp
+Bjorn Canback <bcanback at acgt\&.se>, Dean Laslett <gaiaquark at gmail\&.com >
+.SH "REFERENCES"
+.sp
+Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16
+.sp
+Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
Added: trunk/packages/aragorn/trunk/debian/manpage.1.src
===================================================================
--- trunk/packages/aragorn/trunk/debian/manpage.1.src (rev 0)
+++ trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,166 @@
+ARAGORN(1)
+==========
+
+NAME
+----
+
+aragorn - detect tRNA genes in nucleotide sequences
+
+
+SYNOPSIS
+--------
+
+*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt
+ -gc -tv -seq -br -fasta -fo -o <outfile> <filename>
+
+
+OPTIONS
+-------
+
+ -m Search for tmRNA genes.
+ -t Search for tRNA genes.
+ By default, all are detected. If one of
+ -m or -t is specified, then the other
+ is not detected unless specified as well.
+ -mt Search for Metazoan mitochondrial tRNA genes.
+ tRNA genes with introns not detected. -i,-sr switchs
+ ignored. Composite Metazoan mitochondrial
+ genetic code used.
+ -mtmam Search for Mammalian mitochondrial tRNA
+ genes. -i,-sr switchs ignored. -tv switch set.
+ Mammalian mitochondrial genetic code used.
+ -mtx Same as -mt but low scoring tRNA genes are
+ not reported.
+ -mtd Overlapping metazoan mitochondrial tRNA genes
+ on opposite strands are reported.
+ -gc<num> Use the GenBank transl_table = <num> genetic code.
+ -gcstd Use standard genetic code.
+ -gcmet Use composite Metazoan mitochondrial genetic code.
+ -gcvert Use Vertebrate mitochondrial genetic code.
+ -gcinvert Use Invertebrate mitochondrial genetic code.
+ -gcyeast Use Yeast mitochondrial genetic code.
+ -gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code.
+ -gcciliate Use Ciliate genetic code.
+ -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code
+ -gceuplot Use Euplotid genetic code.
+ -gcbact Use Bacterial/Plant Chloroplast genetic code.
+ -gcaltyeast Use alternative Yeast genetic code.
+ -gcascid Use Ascidian Mitochondrial genetic code.
+ -gcaltflat Use alternative Flatworm Mitochondrial genetic code.
+ -gcblep Use Blepharisma genetic code.
+ -gcchloroph Use Chlorophycean Mitochondrial genetic code.
+ -gctrem Use Trematode Mitochondrial genetic code.
+ -gcscen Use Scenedesmus obliquus Mitochondrial genetic code.
+ -gcthraust Use Thraustochytrium Mitochondrial genetic code.
+ Individual modifications can be appended using
+ ,BBB=<aa> B = A,C,G, or T. <aa> is the three letter
+ code for an amino-acid. More than one modification
+ can be specified. eg -gcvert,aga=Trp,agg=Trp uses
+ the Vertebrate Mitochondrial code and the codons
+ AGA and AGG changed to Tryptophan.
+ -tv Do not search for mitochondrial TV replacement
+ loop tRNA genes. Only relevant if -mt used.
+ -c7 Search for tRNA genes with 7 base C-loops only.
+ -i Search for tRNA genes with introns in
+ anticodon loop with maximum length 3000
+ bases. Minimum intron length is 0 bases.
+ Ignored if -m is specified.
+ -i<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases. Minimum intron length is 0 bases.
+ Ignored if -m is specified.
+ -i<min>,<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases, and minimum length <min> bases.
+ Ignored if -m is specified.
+ -io Same as -i, but allow tRNA genes with long
+ introns to overlap shorter tRNA genes.
+ -if Same as -i, but fix intron between positions
+ 37 and 38 on C-loop (one base after anticodon).
+ -ifo Same as -if and -io combined.
+ -ir Same as -i, but report tRNA genes with minimum
+ length <min> bases rather than search for
+ tRNA genes with minimum length <min> bases.
+ With this switch, <min> acts as an output filter,
+ minimum intron length for searching is still 0 bases.
+ -c Assume that each sequence has a circular
+ topology. Search wraps around each end.
+ Default setting.
+ -l Assume that each sequence has a linear
+ topology. Search does not wrap.
+ -d Double. Search both strands of each
+ sequence. Default setting.
+ -s or -s+ Single. Do not search the complementary
+ (antisense) strand of each sequence.
+ -sc or -s- Single complementary. Do not search the sense
+ strand of each sequence.
+ -ps Lower scoring thresholds to 95% of default levels.
+ -ps<num> Change scoring thresholds to <num> percent of default levels.
+ -rp Report possible pseudogenes (normalised score < 100).
+ -seq Print out primary sequence.
+ -br Show secondary structure of tRNA gene primary sequence
+ using round brackets.
+ -fasta Print out primary sequence in fasta format.
+ -fo Print out primary sequence in fasta format only
+ (no secondary structure).
+ -fon Same as -fo, with sequence and gene numbering in header.
+ -fos Same as -fo, with no spaces in header.
+ -fons Same as -fo, with sequence and gene numbering, but no spaces.
+ -w Print out in Batch mode.
+ -ss Use the stricter canonical 1-2 bp spacer1 and
+ 1 bp spacer2. Ignored if -mt set. Default is to
+ allow 3 bp spacer1 and 0-2 bp spacer2, which may
+ degrade selectivity.\n");
+ -v Verbose. Prints out information during
+ search to STDERR.
+ -a Print out tRNA domain for tmRNA genes.
+ -a7 Restrict tRNA astem length to a maximum of 7 bases
+ -aa Display message if predicted iso-acceptor species
+ does not match species in sequence name (if present).
+ -j Display 4-base sequence on 3' end of astem
+ regardless of predicted amino-acyl acceptor length.
+ -jr Allow some divergence of 3' amino-acyl acceptor
+ sequence from NCCA.
+ -jr4 Allow some divergence of 3' amino-acyl acceptor
+ sequence from NCCA, and display 4 bases.
+ -q Dont print configuration line (which switchs
+ and files were used).
+ -rn Repeat sequence name before summary information.
+ -O <outfile> Print output to <outfile>. If <outfile>
+ already exists, it is overwritten. By default
+ all output goes to stdout.
+
+DESCRIPTION
+-----------
+
+aragorn detects tRNA, mtRNA, and tmRNA genes.
+A minimum requirement is at least a 32 bit compiler architecture
+(variable types int and unsigned int are at least 4 bytes long).
+
+<filename> is assumed to contain one or more sequences
+in FASTA format. Results of the search are printed to
+STDOUT. All switches are optional and case-insensitive.
+Unless -i is specified, tRNA genes containing introns
+are not detected.
+
+
+AUTHORS
+------
+
+Bjorn Canback <bcanback at acgt.se>, Dean Laslett <gaiaquark at gmail.com >
+
+
+REFERENCES
+----------
+
+Laslett, D. and Canback, B. (2004) ARAGORN, a
+program for the detection of transfer RNA and transfer-messenger
+RNA genes in nucleotide sequences
+Nucleic Acids Research, 32;11-16
+
+Laslett, D. and Canback, B. (2008) ARWEN: a
+program to in metazoan mitochondrial
+nucleotide sequences
+Bioinformatics, 24(2); 172-175.
+
+
Added: trunk/packages/aragorn/trunk/debian/patches/formatstrings
===================================================================
--- trunk/packages/aragorn/trunk/debian/patches/formatstrings (rev 0)
+++ trunk/packages/aragorn/trunk/debian/patches/formatstrings 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,20 @@
+--- a/aragorn1.2.34.c
++++ b/aragorn1.2.34.c
+@@ -9276,7 +9276,7 @@
+ else fputc(' ',f); }
+ else
+ fputc('*',f);
+- sprintf(anm," %s %c(%d,%d)",
++ sprintf(anm," %s %c(%ld,%ld)",
+ agene->species,comp[agene->comp],agene->start,agene->stop);
+ fprintf(f,"%-30s ",anm);
+ if (detect[i] >= 0)
+@@ -9347,7 +9347,7 @@
+ else
+ fputc('*',f);
+ fprintf(f," %-33s",agene->species);
+- sprintf(anm,"%c(%d,%d)",comp[agene->comp],agene->start,agene->stop);
++ sprintf(anm,"%c(%ld,%ld)",comp[agene->comp],agene->start,agene->stop);
+ fprintf(f,"%14s ",anm);
+ if (detect[i] >= 0)
+ { sprintf(anm,"%s %s",name(t,nm,1,sw),position(ps,t,sw));
Added: trunk/packages/aragorn/trunk/debian/patches/hardening
===================================================================
--- trunk/packages/aragorn/trunk/debian/patches/hardening (rev 0)
+++ trunk/packages/aragorn/trunk/debian/patches/hardening 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,11 @@
+--- a/aragorn1.2.34.c
++++ b/aragorn1.2.34.c
+@@ -3461,7 +3461,7 @@
+ { fputc('\n',f);
+ i = 1; }
+ if (i > 1) fprintf(f,", ");
+- fprintf(f,thit[nm]); }
++ fprintf(f,"%s",thit[nm]); }
+ fputc('\n',f); }
+ else
+ fprintf(f,"Match with %s tmRNA tag\n",thit[0]); }
Added: trunk/packages/aragorn/trunk/debian/patches/series
===================================================================
--- trunk/packages/aragorn/trunk/debian/patches/series (rev 0)
+++ trunk/packages/aragorn/trunk/debian/patches/series 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,2 @@
+formatstrings
+hardening
Added: trunk/packages/aragorn/trunk/debian/rules
===================================================================
--- trunk/packages/aragorn/trunk/debian/rules (rev 0)
+++ trunk/packages/aragorn/trunk/debian/rules 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+export DESTDIR=$(CURDIR)/debian/tmp
+export DH_ALWAYS_EXCLUDE=.gitignore
+
+include /usr/share/hardening-includes/hardening.make
+
+CFLAGS=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+CFLAGS+=$(HARDENING_CFLAGS)
+LDFLAGS+=$(HARDENING_LDFLAGS)
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ rm -f aragorn
+
+override_dh_auto_build:
+ $(CC) $(CFLAGS) $(LDFLAGS) -trigraphs -o aragorn *.c
+
+override_dh_auto_install:
+ mkdir -p $(DESTDIR)/usr/bin
+ cp aragorn $(DESTDIR)/usr/bin
+
+get-orig-source:
+ bash debian/get-orig-source
Property changes on: trunk/packages/aragorn/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/aragorn/trunk/debian/source/format
===================================================================
--- trunk/packages/aragorn/trunk/debian/source/format (rev 0)
+++ trunk/packages/aragorn/trunk/debian/source/format 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/aragorn/trunk/debian/upstream
===================================================================
--- trunk/packages/aragorn/trunk/debian/upstream (rev 0)
+++ trunk/packages/aragorn/trunk/debian/upstream 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,19 @@
+Name: aragorn
+Contact: Bjorn Canback <bcanback at acgt.se>
+Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
+Reference:
+ Author: Laslett, Dean and Canback, Bjorn
+ Title: >
+ ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide
+ sequences.
+ Journal: Nucleic Acids Research
+ Year: 2004
+ Volume: 32
+ Number: 1
+ Pages: 11-16
+ DOI: 10.1093/nar/gkh152
+ PMID: 14704338
+ URL: http://nar.oxfordjournals.org/content/32/1/11.long
+ eprint: http://nar.oxfordjournals.org/content/32/1/11.full.pdf
+Watch: |
+ http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn(.*).c
Added: trunk/packages/aragorn/trunk/debian/watch
===================================================================
--- trunk/packages/aragorn/trunk/debian/watch (rev 0)
+++ trunk/packages/aragorn/trunk/debian/watch 2013-02-10 14:54:53 UTC (rev 12975)
@@ -0,0 +1,9 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn(.*).c
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