debian/0000755000000000000000000000000012262753171007174 5ustar debian/bin/0000755000000000000000000000000012214301210007720 5ustar debian/bin/arb_create_debian_conffile0000644000000000000000000000074712214301210015111 0ustar #!/bin/sh exit 0 # Do nothing for the moment ... set -e PROG=arb GROUP=${PROG} CONFFILE=/etc/${PROG}/${PROG}_tcp.dat CATTEMPLATES="/etc/${PROG}/${PROG}_tcp_template.dat /etc/${PROG}/${PROG}_ntree.dat /etc/${PROG}/${PROG}_pt_server.dat" CATFILES="" for catfile in ${CATTEMPLATES} ; do if [ -e $catfile ] ; then CATFILES="$CATFILES $catfile" ; fi done cat ${CATFILES} > ${CONFFILE} chgrp ${GROUP} /etc/${PROG}/${PROG}_*.dat chmod 664 /etc/${PROG}/${PROG}_*.dat debian/bin/arb-add-pt-server0000644000000000000000000000377212214301210013073 0ustar #!/usr/bin/perl # Allow users of group "arb" to add pt_server entries # Andreas Tille # License: GPL use warnings; use strict; use POSIX; my $group2seek = "arb" ; my $seekgroup = getgrnam($group2seek) ; my @PTServerLines = () ; my %PTEntry; my $PTServerDir = "/var/lib/arb/pts" ; my @ptservers; my $user = getpwuid($<) ; if ( ! $seekgroup ) { print STDERR "Group $group2seek does not exist.\n" ; exit -1 ; } $_ = $( ; if ( ! /\b$seekgroup\b/ ) { print STDERR "User $user is not member of group $group2seek.\n" ; exit(-1) ; } my $cfgfile = "/etc/arb/arb_tcp.dat" ; # my $cfgfile = "/etc/arb/arb_pt_server.dat" ; my $tmpfile = tmpnam(); open ( CFG, $cfgfile ) || die ( "Unable to open Arb config file $cfgfile." ) ; open ( TMP, ">$tmpfile" ) || die ( "Unable to open temporary file $tmpfile for writing." ) ; my ( $i, $port, $path, $i_max, $port_max ) ; $i_max = $port_max = 0; while ( ) { if ( ! /^[^#]*\bARB_PT_SERVER/ ) { print TMP ; next ; } chomp ; s/\s*#.*// ; if ( /ARB_PT_SERVER([0-9]+)\s+localhost:([0-9]{4})\s+arb_pt_server\s+-D(.+)$/ ) { $i = $1; $port = $2; $path = $3; print "$i: $port, $path\n" ; if ( $i > $i_max ) { $i_max = $i ; } if ( $port > $port_max ) { $port_max = $port ; } } else { print "Canot parse PT_SERVER entry: $_\n" ; } @PTServerLines = (@PTServerLines, $_) ; } my $pts ; foreach $pts ( @PTServerLines ) { print TMP "$pts\n" ; } print STDERR "Verify existing Servers in $PTServerDir.\n" ; if ( ! opendir(DIR, $PTServerDir) ) { print STDERR "PT-Server directory $PTServerDir does not exist.\n" ; exit -1 ; } @ptservers = grep { /^$user[0-9]+\.arb$/ } readdir(DIR); closedir DIR; my $pts_usermax = 0; foreach $pts ( @ptservers ) { if ( $pts =~ /$user([0-9]+)\.arb/ ) { if ( $1 > $pts_usermax ) { $pts_usermax = $1 ; } } } $pts_usermax += 1 ; system ("touch $PTServerDir/$user$pts_usermax.arb"); close TMP ; print "$i_max, $port_max\n" ; system ("mv $tmpfile tempfile.dat"); debian/bin/arb.10000644000000000000000000000212612214301210010547 0ustar '\" t .\" ** The above line should force tbl to be a preprocessor ** .\" Copyright (C), 2001, Andreas Tille .\" .\" You may distribute under the terms of the GNU General Public .\" License as specified in the file COPYING that comes with the .\" man_db distribution. .\" .\" .TH Arb 1 "November 17, 2004" "ARB" .SH NAME .B arb \- various tools for sequence database handling and data analysis .SH SYNOPSIS .B arb .SH DESCRIPTION This is the Debian GNU/Linux version of Arb. The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. For a more detailed description see the Arb homepage http://rtfm.arb-home.de/ .SH SEE ALSO arb-add-pt-server(), arb_clean(), arb-kill(1), arb_ntree(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/bin/arb0000644000000000000000000000275412214301210010417 0ustar #!/bin/sh CONF=/etc/arb/arb.conf USERCONF=${HOME}/.arb.conf USERPROP=${HOME}/.arb_prop [ -s $CONF ] && . $CONF # override general settings with user specific settings [ -s $USERCONF ] && . $USERCONF # Try to make user working directory for arb data if [ _"$ARBUSERDATA" != _"" ] ; then if [ ! -d $ARBUSERDATA ] ; then mkdir -p $ARBUSERDATA || ARBUSERDATA="" fi fi if [ _"$ARBUSERDATA" != _"" ] ; then cd $ARBUSERDATA if [ ! -s demo.arb ] ; then if [ -s /usr/share/doc/arb/examples/demo.arb.gz ] ; then cp -a /usr/share/doc/arb/examples/demo.arb.gz . gunzip demo.arb.gz fi fi fi # if user has no arb input masks just symlink to the sample masks [ -d "$USERPROP/inputMasks" ] || mkdir -p "$USERPROP/inputMasks" MASKS=`ls "$USERPROP/inputMasks" | wc -l` if [ $MASKS -eq 0 ] ; then cd "$USERPROP/inputMasks" for mask in `ls /usr/lib/arb/lib/inputMasks/*.mask` ; do ln -s $mask . done fi # Save files as group readable umask 002 # Warn if the user is not member of group arb and thus not allowed to write # to /var/lib/arb subdirectories if ! groups | grep -q -w arb ; then cat < .\" .\" You may distribute under the terms of the GNU General Public .\" License as specified in the file COPYING that comes with the .\" man_db distribution. .\" .\" .TH arb-add-pt-server 1 "November 17, 2004" "Arb add PT_Server" .SH NAME .B arb-add-pt-server \- enable users to maintain their arb PT_Server databases .SH SYNOPSIS .B arb-add-pt-server .SH DESCRIPTION On Debian GNU/Linux systems this script adds a new (empty) PT_Server database to the arb PT_Server repository and adds an entry to the relevant config file provided that the user belongs to the group arb. .SH SEE ALSO arb(1), arb_clean(1), arb-kill(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/bin/arb_clean.10000644000000000000000000000137612214301210011717 0ustar '\" t .\" ** The above line should force tbl to be a preprocessor ** .\" Copyright (C), 2001, Andreas Tille .\" .\" You may distribute under the terms of the GNU General Public .\" License as specified in the file COPYING that comes with the .\" man_db distribution. .\" .\" .TH arb_clean 1 "November 17, 2004" "Clean arb processes" .SH NAME .B arb_clean \- clean processes started by arb that are started by the user .SH SYNOPSIS .B arb_clean .SH DESCRIPTION Sometimes arb leaves some processes running. All processes which are cleanly registered by arb will be killed. .SH SEE ALSO arb-kill(), arb(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/bin/arb-kill0000644000000000000000000000143412214301210011342 0ustar #!/bin/sh arb_clean if [ _"$1" != _"--all" ] ; then # grep only the processes owned by $USER kill -9 `ps aux | grep -w "^${USER}" | grep -v "0:0[0-9] grep " | grep -v "0:0[0-9] ps " | \ grep -w -e arb -e arb_ntree | \ grep -v nxagent | \ sed "s/^${USER}[[:space:]]\+\([0-9]\+\)[[:space:]]\+.*/\1/"` for arbpid in /tmp/arb_pids_${USER}_* ; do if [ -f "$arbpid" ] ; then rm -f "$arbpid" fi done else # # if option --all was given kill all processes trying sudo sudo kill -9 `ps aux | grep -v "0:0[0-9] grep " | grep -v "0:0[0-9] ps " | \ grep -w -e arb -e arb_ntree | \ grep -v nxagent | \ sed "s/^[a-z0-9]\+[[:space:]]\+\([0-9]\+\)[[:space:]]\+.*/\1/"` for arbpid in /tmp/arb_pids_*_* ; do if [ -f "$arbpid" ] ; then rm -f "$arbpid" fi done fi debian/bin/arb-kill.10000644000000000000000000000161312214301210011500 0ustar '\" t .\" ** The above line should force tbl to be a preprocessor ** .\" Copyright (C), 2001, Andreas Tille .\" .\" You may distribute under the terms of the GNU General Public .\" License as specified in the file COPYING that comes with the .\" man_db distribution. .\" .\" .TH arb-kill 1 "November 17, 2004" "Kill arb processes" .SH NAME arb-kill \- definitely kill all processes started by arb that are started by the user If option --all is given try sudo to kill all processes even if they are owned by other users. .SH SYNOPSIS .B arb-kill [--all] .SH DESCRIPTION Sometimes arb leaves some processes running. All processes that belong to the user who is calling arb-kill will be killed. .SH SEE ALSO arb_clean(), arb(1), kill(1), sudo(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/arb-common.links0000644000000000000000000000074112214301210012246 0ustar etc/arb/ARB_GDEmenus usr/lib/arb/GDEHELP/ARB_GDEmenus var/lib/arb/pts usr/lib/arb/lib/pts var/lib/arb/nas usr/lib/arb/lib/nas usr/lib/arb/SH/arb_clean usr/bin/arb_clean usr/share/doc/arb/html usr/lib/arb/lib/help_html usr/share/doc/arb/submit usr/lib/arb/lib/submit usr/share/arb/lib/pictures usr/lib/arb/lib/pictures usr/share/arb/lib/pixmaps usr/lib/arb/lib/pixmaps usr/share/arb/lib/rna3d usr/lib/arb/lib/rna3d debian/About0000644000000000000000000000333512214301210010151 0ustar Initially, ARB was developed for rRNA data, however, the package also supports handling and analysis of protein coding genes. Currently, the ARB software is under further development for genome sequence database management. Highlighted features: - Any database entry can be visualised in the main window along with a phylogenetic tree. Database access and navigation is possible via mouse click in the displayed tree or by using a search tool. - Sequence and additional data can be im- and exported in a variety of commonly used flat file formates. - A powerfull editor for real or virtual primary structures includes versatile tools for string searching, automated alignment of primary structures, local alignment optimisation, automated secondary structure check as well as secondary structure visualisation. - Conservation profiles and column filters can be established according to user defined criteria applying different procedures. - Distance matrix, maximum parsimony and maximum likelihood based phylogenetic treeing can be performed applying the respective integrated tools. A special maximum parsimony approach allows reconstruction and optimisation of comprehensive trees representing the full sequence data set (currently more than 20.000 entries). - Publication ready trees can be generated and exported in various formates. - The ARB PT server (positional tree) provides the basis for rapid searching closest relatives or specific sequence signatures. Such signatures can be evaluated as taxon specific probes against the background of the full database. - The ARB project maintains processed databases for ribosomal RNAs and selected evolutionary conserved genes. debian/arb.menu0000644000000000000000000000020712214301210010601 0ustar ?package(arb):needs="X11" section="Applications/Science/Biology" \ title="Arb" icon="/usr/share/arb/arb.xpm" command="/usr/bin/arb" debian/arb.prerm0000644000000000000000000000020112214301210010754 0ustar #!/bin/sh set -e PROG=arb CONFFILE=${PROG}_tcp.dat ARBLIBDIR=/usr/lib/${PROG}/lib rm -rf ${ARBLIBDIR}/${CONFFILE} #DEBHELPER# debian/libarb.dirs0000644000000000000000000000003412214301210011263 0ustar usr/share/lintian/overrides debian/arb.postinst0000644000000000000000000000111212214301210011514 0ustar #!/bin/sh set -e PROG=arb GROUP=${PROG} CONFFILE=/etc/${PROG}/${PROG}_tcp.dat ## Add group ${PROG} if not existent TESTGROUP="`getent group ${GROUP}`" || true if [ -z "${TESTGROUP}" ] ; then addgroup --system "${GROUP}" >/dev/null fi if [ -e /usr/share/${PROG}/SH/arb_create_debian_conffile ] ; then /usr/share/${PROG}/SH/arb_create_debian_conffile fi ARBLIBDIR=/usr/lib/${PROG}/lib/ if [ ! -d ${ARBLIBDIR} ] ; then mkdir -p ${ARBLIBDIR} fi if [ ! -L ${ARBLIBDIR}/`basename ${CONFFILE}` ] ; then ln -s ${CONFFILE} ${ARBLIBDIR}/`basename ${CONFFILE}` fi #DEBHELPER# debian/copyright0000644000000000000000000002441612247564362011143 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Arb Upstream-Contact: Arb development team , Ralf Westram Source: http://download.arb-home.de/release/ Files: * Copyright: 1994-2011 Department of Microbiology: - Dr. Wolfgang Ludwig (Biologist) Task: Group Leader; Inventor of ARB, knows everything about it - Ralf Westram (Computer scientist) Task: General ARB development - Dr. Lothar Richter (Biologist) Task: ARB Database Curation and Automatization - Arno Buchner (Biologist) Task: ARB Database Curation and Genomics . Department of Computer Science: - Prof. Dr. Thomas Ludwig Task: Computer Science Supervisor - Dr. Harald Meier (Biologist) Task: ARB GENOME programming - Gangolf Jobb (Biologist) Task: Development and integration of alignment- and tree-generation-software License: ARB * The ARB software and documentation are not in the public domain. * External programs distributed together with ARB are copyrighted by and are the property of their respective authors unless otherwise stated. * All other copyrights are owned by Lehrstuhl fuer Mikrobiologie, TU Muenchen. . USAGE LICENSE . You have the right to use this version of ARB for free. Please read as well the attached copyright notices below whether you may or may not install this package. . REDISTRIBUTION LICENSE . * This release of the ARB program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without the expressed written consent of the Technical University of Munich and of its supervisors Oliver Strunk, Ralf Westram & Wolfgang Ludwig. * All interested parties may redistribute and modify ARB as long as all copies are accompanied by this license information and all copyright notices remain intact. Parties redistributing ARB must do so on a non-profit basis, charging only for cost of media. * If you modify parts of ARB and redistribute these changes the 'Lehrstuhl fuer Mikrobiologie' gains the right to incorporate these changes into ARB and to redistribute them with future versions of ARB. . Disclaimer . THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. User understands the software is a research tool for which no warranties as to capabilities or accuracy are made, and user accepts the software "as is." User assumes the entire risk as to the results and performance of the software and documentation. The above parties cannot be held liable for any direct, indirect, consequential or incidental damages with respect to any claim by user or any third party on account of, or arising from the use of software and associated materials. This disclaimer covers both the ARB core applications and all external programs used by ARB. . Additional not for Debian packaging: . Hereby anybody is granted the right to build debian-pakets of the ARB software package (http:://www.arb-home.de/) and publish them on debian mirrors (or any other way of debian-distribution). . This includes any debian derivates like ubuntu. . The ARB developers may (but most likely wont ever) revoke this granting. If really done so, it'll only affect ARB versions released after such a revocation. . 9. July 2008 Ralf Westram Files: GDE/* Copyright: 2004-2008 The Board of Trustees of the University of Illinois and by Steven Smith License: GDE * The Genetic Data Environment (GDE) software and documentation are not in the public domain. Portions of this code are owned and copyrighted by the The Board of Trustees of the University of Illinois and by Steven Smith. External functions used by GDE are the property of their authors. This release of the GDE program and documentation may not be sold, or incorporated into a commercial product, in whole or in part without the expressed written consent of the University of Illinois and of its author, Steven Smith. * All interested parties may redistribute the GDE as long as all copies are accompanied by this documentation, and all copyright notices remain intact. Parties interested in redistribution must do so on a non-profit basis, charging only for cost of media. Modifications to the GDE core editor should be forwarded to the author Steven Smith. External programs used by the GDE are copyrighted by, and are the property of their respective authors unless otherwise stated. Files: GDE/PHYLIP/* Copyright: (c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington. License: PHYLIP_non-free Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. Comment: Remark from the Debian package maintainer Andreas Tille Phylp is not used in the binary package because the Debian package is used which is in the non-free part of Debian. Remark: After heavy discussion with the author of Phylip it was not possible to convince him to use a free license. Files: GDE/SUPPORT/CAP2.c Copyright: (C) 1991 Xiaoqiu Huang License: CAP2_non-free The distribution of the program is granted provided no charge is made and the copyright notice is included. Comment: Remark from the Debian package maintainer Andreas Tille I was unable to find a source URL where this program which is claimed as external can be downloaded. Files: CONVERTALN/* Copyright: (C) 1992 Wen-Min Kuan License: ARP_permissive The files in this directory do not contain an explicite license statement. It has to be assumed that the license is the same as the general usage and redistribution license for Arb and the authors of Arb got a permission to distribute this code in their product. . This paragraph was just added to the copyright file to mention that there is some copyrighted work which was not mentioned above. Comment: convert_aln -- an alignment(or sequence) converter written by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992. . Remark from the Debian package maintainer Andreas Tille: I was unable to find a source URL where this program which is claimed as external can be downloaded. Files: GDE/FASTDNAML/* Copyright: (C) 1998, 1999, 2000 by Gary J. Olsen, 1986 - 1990 by the University of Washington and Joseph Felsenstein. License: GPL Comment: Remark from the Debian package maintainer Andreas Tille: This is not used in the binary package because it is available as official Debian package and has a free license (see this package). Files: GDE/RAxML/a* Copyright: (C) 2004-2008 Alexandros Stamatakis, Michael Ott, Thomas Ludwig License: GPL Comment: There is also a file GDE/RAxML/softwaredisclaimer in this directory which contains some license text which might be provided in a private mail or whatever from the RAxML authors to the Arb authors. The relevance of this file is completely unclear because RAxML as it can be obtained from http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm is GPLed and the remaining files in this directory are neither copyrighted by the RAxML authors nor do they feature a similar license statement. This file is subject for clarification by the Arb authors. Files: GDE/RAxML/c* GDE/RAxML/d* GDE/RAxML/p* Copyright: (C) 1993-2002 by the University of Washington. Written by Joseph Felsenstein, Hisashi Horino, and others License: RAxML_non-free Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. Files: GDE/RAxML/g* Copyright: (C) 1987, 1993, 1994 The Regents of the University of California. All rights reserved. License: BSD Copyright (c) The Regents of the University of California. All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: GDE/TREEPUZZLE/* Copyright: (C) 1995-1999 Korbinian Strimmer and Arndt von Haeseler (C) 1999-2001 Heiko A. Schmidt, Korbinian Strimmer,Martin Vingron, Arndt von Haeseler License: GPL Comment: This code is not used in the binary package because it is available as official Debian package and has a free license (see this package). Files: READSEQ/* Copyright: 1990-1993 D. Gilbert License: PD readseq is public domain software Comment: This code is not used in the binary package because it is available as official Debian package and has a free license (see this package). Files: debian/* Copyright: (C) 2008-2013 Andreas Tille License: GPL License: GPL On Debian systems, the complete text of the GNU Public License can be found in `/usr/share/common-licenses/GPL-2'. debian/arb.links0000644000000000000000000000402612214301210010760 0ustar usr/bin/readseq usr/lib/arb/bin/arb_readseq usr/lib/phylip/bin/clique usr/lib/arb/bin/clique usr/bin/clustalw usr/lib/arb/bin/clustalw usr/lib/phylip/bin/consense usr/lib/arb/bin/consense usr/lib/phylip/bin/contml usr/lib/arb/bin/contml usr/lib/phylip/bin/contrast usr/lib/arb/bin/contrast usr/lib/phylip/bin/dnacomp usr/lib/arb/bin/dnacomp usr/lib/phylip/bin/dnadist usr/lib/arb/bin/dnadist usr/lib/phylip/bin/dnainvar usr/lib/arb/bin/dnainvar usr/lib/phylip/bin/dnaml usr/lib/arb/bin/dnaml usr/lib/phylip/bin/dnamlk usr/lib/arb/bin/dnamlk usr/lib/phylip/bin/dnamove usr/lib/arb/bin/dnamove usr/lib/phylip/bin/dnapars usr/lib/arb/bin/dnapars usr/lib/phylip/bin/dnapenny usr/lib/arb/bin/dnapenny usr/lib/phylip/bin/dollop usr/lib/arb/bin/dollop usr/lib/phylip/bin/dolmove usr/lib/arb/bin/dolmove usr/lib/phylip/bin/dolpenny usr/lib/arb/bin/dolpenny usr/lib/phylip/bin/drawgram usr/lib/arb/bin/drawgram usr/lib/phylip/bin/drawtree usr/lib/arb/bin/drawtree usr/lib/phylip/bin/factor usr/lib/arb/bin/factor usr/lib/phylip/bin/fitch usr/lib/arb/bin/fitch usr/lib/phylip/bin/gendist usr/lib/arb/bin/gendist usr/lib/phylip/bin/kitsch usr/lib/arb/bin/kitsch usr/lib/phylip/bin/mix usr/lib/arb/bin/mix usr/lib/phylip/bin/move usr/lib/arb/bin/move usr/lib/phylip/bin/neighbor usr/lib/arb/bin/neighbor usr/lib/phylip/bin/pars usr/lib/arb/bin/pars usr/lib/phylip/bin/penny usr/lib/arb/bin/penny usr/lib/phylip/bin/proml usr/lib/arb/bin/proml usr/lib/phylip/bin/promlk usr/lib/arb/bin/promlk usr/lib/phylip/bin/protdist usr/lib/arb/bin/protdist usr/lib/phylip/bin/protpars usr/lib/arb/bin/protpars usr/bin/tree-puzzle usr/lib/arb/bin/puzzle usr/lib/phylip/bin/restdist usr/lib/arb/bin/restdist usr/lib/phylip/bin/restml usr/lib/arb/bin/restml usr/lib/phylip/bin/retree usr/lib/arb/bin/retree usr/lib/phylip/bin/seqboot usr/lib/arb/bin/seqboot usr/lib/phylip/bin/treedist usr/lib/arb/bin/treedist usr/bin/fastDNAml usr/lib/arb/bin/fastdnaml usr/bin/protml usr/lib/arb/bin/protml debian/arb-common.preinst0000644000000000000000000000106612214301210012613 0ustar #!/bin/sh set -e # Reason: When upgrading from a pre-0.0.20050526-4 version a directory # /usr/share/arb/lib/nas exists and prevents setting the symlink from # the package correctly. Thus this directory has to be removed first dirtoremove=/usr/share/arb/lib/nas case "$1" in upgrade) if [ ! -L $dirtoremove ] ; then if [ -d $dirtoremove ] ; then # Just rmdir the directory, if there should be some user # files the user get's the information to clean the # directory by the error message rmdir $dirtoremove fi fi ;; esac #DEBHELPER# debian/arb-common.lintian-overrides0000644000000000000000000000025112214301210014560 0ustar # This script is not intended to be run by itself. Instead # it is used to construct a script at runtime arb-common: script-not-executable ./usr/lib/arb/lib/macro.head debian/arb-doc.install0000644000000000000000000000015412214301210012047 0ustar HELP_SOURCE/oldhelp/arb.pdf.gz usr/share/doc/arb/help lib/help_html/* usr/share/doc/arb/html debian/arb-common.postinst0000644000000000000000000000246112214301210013012 0ustar #!/bin/sh set -e PROG=arb GROUP=${PROG} DEBCONF_DEBUG=developer . /usr/share/debconf/confmodule db_version 2.0 db_get ${PROG}/group retusers=${RET} db_go || true CURRENTGROUPUSERS=`getent group ${GROUP} | sed "s/.*:\([^:]*\)/\1/" | tr ',' '\n'` # Add those users which were selected but are not yet in the group for user in `echo "$retusers" | sed "s/([^)]*)//g" | sed "s/ //g" | tr ',' '\n'` ; do if ! `echo "${CURRENTGROUPUSERS}" | grep -q -w "$user"` ; then adduser $user $GROUP fi done # Del those users which were obviousely removed from list of ${PROG} users for user in ${CURRENTGROUPUSERS} ; do if ! `echo "$retusers" | grep -q -w "$user"` && \ `getent group "$GROUP" | grep -q -w $user` ; then deluser $user $GROUP fi done ptsdir=/var/lib/${PROG}/pts # Make sure that demo pts-server file can be accesed by members of group arb [ -d ${ptsdir} ] || mkdir -p ${ptsdir} ptsdemo=${ptsdir}/demo.arb # Create empty pts-server demo file touch $ptsdemo chgrp ${GROUP} $ptsdemo chmod 664 $ptsdemo # Make sure that users in group arb are able to write to pts-server dir chgrp ${GROUP} $ptsdir chmod 775 $ptsdir nasdir=/var/lib/${PROG}/nas # Make sure that nameserver can be accesed by members of group arb [ -d ${nasdir} ] || mkdir -p ${nasdir} chgrp ${GROUP} $nasdir chmod 775 $nasdir #DEBHELPER# debian/arb-common.install0000644000000000000000000000206412214301210012574 0ustar GDEHELP/ARB_GDEmenus etc/arb GDEHELP/DATA_FILES usr/lib/arb/GDEHELP HELP_SOURCE/oldhelp/*.hlp usr/lib/arb/HELP_SOURCE/oldhelp HELP_SOURCE/oldhelp/prompt usr/lib/arb/HELP_SOURCE/oldhelp PERL2ARB/ARB.pm usr/lib/arb/lib PERL_SCRIPTS usr/lib/arb SH/[a-z]* usr/lib/arb/SH debian/About usr/share/doc/arb/ debian/bin/arb_create_debian_conffile usr/lib/arb/SH demo.arb usr/share/doc/arb/examples lib/[d-gi-kmoqt-z]* usr/lib/arb/lib lib/arb_default/* usr/lib/arb/lib/arb_default lib/help usr/lib/arb/lib lib/nas/names.dat* var/lib/arb/nas lib/pi* usr/share/arb/lib lib/pts var/lib/arb lib/rna3d usr/share/arb/lib lib/s[a-tv-z]* usr/lib/arb/lib lib/submit usr/share/doc/arb debian/libarb.lintian-overrides0000644000000000000000000000020712214301210013762 0ustar # rpath is set intentionally to make use of private dynamic # libraries libarb: binary-or-shlib-defines-rpath ./usr/lib/arb/lib/ARB.so debian/arb-common.templates0000644000000000000000000000030412214301210013117 0ustar Template: arb/group Type: multiselect Choices: ${users} _Description: Arb users: Please choose, among the list of all unprivileged users of the system, those who will be allowed running ${pkg}. debian/changelog0000644000000000000000000004736512262753160011063 0ustar arb (5.5-5ubuntu1) trusty; urgency=medium * Rebuild against glew 1.10. * Fix build with recent GL (?), Motif (?). -- Matthias Klose Tue, 07 Jan 2014 09:05:19 +0100 arb (5.5-5) unstable; urgency=low * build-depend on libtiff-dev instead of libtiff4-dev (thanks for the patch to Logan Rosen ) Closes: #729769 * cme fix dpkg-control * cme fix dpkg-copyright * canonical Vcs fields * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Wed, 04 Dec 2013 09:24:14 +0100 arb (5.5-4) unstable; urgency=low * Build-Depends: libglew-dev instead of libglew1.5-dev Closes: #714327 -- Andreas Tille Fri, 28 Jun 2013 09:42:35 +0200 arb (5.5-3) unstable; urgency=low * debian/control: - Restrict arb to architectures amd64 i386 kfreebsd-i386 kfreebsd-amd64 because only there raxml is fullfilled. This makes sense because arb will most probably used only on these architectures anyway. Closes: #714268 - Remove Dependency from openjdk which is not needed any more according to upstream * debian/arb-common.README.debian: Explain restriction to certain architectures * debian/arb.README.debian: Updated about architecture restriction and other things -- Andreas Tille Thu, 27 Jun 2013 14:52:57 +0200 arb (5.5-2) unstable; urgency=low [ Tim Booth ] * debian/rules: Make sure arb_edit4 will be really built and abort package building process if not [ Andreas Tille ] * Rebuild against libmotiv-dev in main Closes: #713061 * Add 4.6.3, 4.7.3 and 4.8.[0-3] to ALLOWED_GCC_VERSIONS Closes: #713219 * debian/control: - remove DM-Upload-Allowed - Build-Depends: libglu1-mesa-dev - add raxml to Depends and do not build third party copy any more (debian/patches/60_use_debian_packaged_raxml.patch) * debian/patches/*: DEP3 comments * debian/patches/50_build_naligner.patch: Fix build issue that was caused by some brocken $(CFLAGS) * debian/rules: use xz compression -- Andreas Tille Mon, 24 Jun 2013 09:42:03 +0200 arb (5.5-1) unstable; urgency=low * New upstream version (+adapted patches) * Standards-Version: 3.9.4 (no changes needed) * debian/po: Add Slovak po-debconf translation (Thanks to Slavko for the translation) Closes: #686275 * debian/rules: Add '-lm' as suggested in patch by Konstantinos Margaritis to fix the build problem on armhf. This together with new upstream closes: #692499 -- Andreas Tille Tue, 11 Dec 2012 09:59:08 +0100 arb (5.3-4) unstable; urgency=low * debian/upstream: Add citations * debian/control: - Build-Depends: libpng-dev instead of libpng12-dev Closes: #662270 - Standards-Version: 3.9.3 (no changes needed) * debian/po/nl.po: Add Dutch translation of debconf templates Thanks for the translation to Jeroen Schot Closes: #654763 * debian/patches/30_Makefile_main: - Enable gcc-4.7 as well Closes: #682404 - Enable using hardening flags * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue * debhelper 9 (control+compat) * debian/rules: - Fixed clean target - propagate hardening flags -- Andreas Tille Thu, 26 Jul 2012 12:15:21 +0200 arb (5.3-3) unstable; urgency=low * debian/control: - Build-Depends: time Strangely enough this is not needed in local pbnuilder/sbuild environments but on autobuilders this seems to be a problem according to comparing the build logs - Build-Depends: libbio-perl-perl Otherwise some not-critical checks will fail * debian/arb.prerm: Care for removal of conffile link created in postinst Closes: #656035 * debian/rules: - clean up some manual handling of files and dirs which is not needed any more with recent versions - insert check which verifies that binary-indep target is really builded and changed files and dirs are previousely created Closes: #658691 -- Andreas Tille Thu, 09 Feb 2012 13:44:22 +0100 arb (5.3-2) unstable; urgency=low * debian/arb.README.Debian: Dropped molphy related notice * debian/control: - Remove Build-Depends: x11proto-print-dev - Remove at least explicite Build-Depends: libxp-dev Closes: #623638 * debian/{control,rules}: Remove quilt which is unneeded when using source format 3.0 (quilt) * debian/po/ca.po: Catalan translation (thanks to Innocent De Marchi ) Closes: #632206 -- Andreas Tille Thu, 15 Dec 2011 17:00:46 +0100 arb (5.3-1) unstable; urgency=low [ Nelson A. de Oliveira ] * Fix FTBFS: replaced sablotron by xsltproc in debian/control (Closes: #634999) * Replaced arb dependency on the ssh metapackage by openssh-client only [ Andreas Tille ] * New upstream version (including updateing debian/patches/*) This version doese not depend from molphy any more * debian/control - Do not depend from molphy which is removed from Debian any more - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields * Debhelper 8 (control+compat) * debian/copyright: several DEP5 fixes -- Andreas Tille Fri, 11 Nov 2011 11:46:22 +0100 arb (5.2-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) * New debconf translations - Vietnamese (thanks to Clytie Siddall ) Closes: #576020 - Danish (thanks to Joe Dalton ) Closes: #584283 - Brazilian Portuguese (thanks to Gustavo Jordan ) Closes: #596647 * Drop xview-clients Suggests in debian/control and replace any occurence of textedit (which is part of xview-clients) by editor via debian/patches/no_xview_dependency.patch Closes: 612534 * debian/patches/20_Makefiles: clean up some errors in clean target * debian/patches/20_config.makefiles: Really get the DEB_BUILD_ARCH_BITS applied * Build-Depends: time -- Andreas Tille Wed, 09 Feb 2011 16:56:15 +0100 arb (5.1-1) unstable; urgency=low [ Andreas Tille ] * New upstream version Closes: #522021 * debian/control: - Package arb-doc in non-free/doc - Standards-Version: 3.8.4 (Added README.source) - Build-Depends: dpkg-dev (>= 1.15.4) to make use of `dpkg-architecture -qDEB_BUILD_ARCH_BITS` in Makefile - Build-Depends: xutils-dev - arb Recommends: bioperl - arb Suggests: phyml - Build-Depends: openjdk-6-jdk instead of kaffe which might be subject of removal from Debian in the near future * Removed / changed patches which were applied upstream - debian/patches/ARB_release200712_gcc4.3.1.patch removed - debian/patches/20_replace_rxp_by_xmllint.patch removed - debian/patches/tmpfile_CVE-2008-5378.patch removed applied part * debian/{rules,*.install}: Cleanup regarding changes in new upstream version * debian/arb.README.debian: - Removed useless warning about prereleases - Added hint about different phyml versions * debian/patches/10_gcc_4.4.3.patch: compile with gcc-4.4.3 * debian/rules: Add ARBHOME variable explicitly to clean target * Added Finish debconf translation (Thanks to Esko Arajärvi ) Closes: #536516 * Added Galician debconf translation (Thanks to marce ) Closes: #537534 * Added Japanese debconf translation (Thankse to Hideki Yamane ) Closes: #554882 * Added: Spanish debconf translation (Thanks to Francisco Javier Cuadrado ) Closes: #573005 * Switch to source format 3.0 [ David Paleino ] * Removed myself from Uploaders * New watch file -- Andreas Tille Tue, 23 Mar 2010 14:37:30 +0100 arb (0.0.20071207.1-7) unstable; urgency=low * Bumped debhelper to version 7 -> dh_clean -k -> dh_clean; dh_prep * Standards-Version: 3.8.1 (no changes needed) * Enhanced package description of arb-common and arb-doc Closes: #517710 * Added Portuguese translation for debconf messages (thanks to Traduz ) Closes: #516958 * Added Depends: ${misc:Depends} to all packages -- Andreas Tille Fri, 20 Mar 2009 08:14:21 +0100 arb (0.0.20071207.1-6) unstable; urgency=low * Save use of /tmp in arb-kill and addressing the other potential tempfile symlink attacks reported in CVE-2008-5378: possible symlink attacks Closes: #508942 * Use xmllint instead of rxp to verify helpfile XML because rxp is outdate, unmaintained and should be removed. * Do not use command-with-path-in-maintainer-script in postinst and config * Added Russian debconf translation (Thanks to Yuri Kozlov) Closes: #511376 -- Andreas Tille Tue, 10 Feb 2009 23:32:41 +0100 arb (0.0.20071207.1-5) unstable; urgency=low * Fix tempfile issues in upstream scripts Closes: #496396 * Fix arb name server location in config file (Thanks to Felipe Figueiredo ) Closes: #495650 * arb-common.config: Make sure that config file will not fail when NIS is used -- Andreas Tille Tue, 23 Sep 2008 13:32:05 +0200 arb (0.0.20071207.1-4) unstable; urgency=low * debian/arb-common.postrm: Remove stuff arb leaves behind in /var/lib in case the package is purged Closes: #463010 * More precise copyright / license statements in debian/copyright * debian/arb-doc.lintian-overrides: Explain why arb-doc should not be in section doc * Moved debian/*.lintian.overrides to *.lintian-overrides and make use of dh_lintian (includes increasing versioned depends of debhelper to >= 6.0.7) * Strip rpath from ARB.so using chrpath * Better short description which was to generic after [Biology] marker was removed. -- Andreas Tille Wed, 23 Jul 2008 08:10:46 +0200 arb (0.0.20071207.1-3) unstable; urgency=low [ Charles Plessy ] * Changed the doc-base section according to the new policy. [ Andreas Tille ] * Updated dependency from libglew (Build-Depends: libglew-dev -> libglew1.5-dev) Closes: #489330 * Standards-Version: 3.8.0 (no changes needed) * debian/patches/30_Makefile_main: Enable gcc-4.3 * Applied upstream patches to compile with gcc-4.3 (thanks to Ralf Westram ) -- Andreas Tille Mon, 07 Jul 2008 09:11:40 +0200 arb (0.0.20071207.1-2) unstable; urgency=low * Added XS-Autobuild: yes to enable autobuilding * Slightly enhanced description -- Andreas Tille Thu, 06 Mar 2008 23:23:07 +0100 arb (0.0.20071207.1-1) unstable; urgency=low [ David Paleino ] * debian/control: - Standards-Version 3.7.3 - long lines wrapped - architecture set to "any" for architecture-dependent packages - fixed some typos in long descriptions - removed [Biology] pseudo-tag from short descriptions -- why not using DebTags? - updated Vcs-* fields - added myself to Uploaders - removing XS- from DM-Upload-Allowed * debian/watch added * debian/po/it.po added * debian/rules updated [ Andreas Tille ] * New upstream source debian/get-orig-source: Obtain official release. Remark: The originally downloaded source from 2007_12_07 was different from the currently available one. This is expressed in the additional ".1" in the version number. * Removed warning from long description because this is now an official release * debian/rules: - removed get-orig-source.old target - added missing '-' in clean target * Switched to quilt (dpatch was not able to apply patches from previous version) -- Andreas Tille Mon, 25 Feb 2008 09:34:30 +0100 arb (0.0.20071207-1) unstable; urgency=low * New upstream version Closes: #446666 * Added Build-Depends libglew-dev which is needed for 3D version * Added Build-Depends libxpm4-dev according to the advise of Charles Plessy in bug #364908 * Added x11proto-print-dev, libxpm-dev, libxp-dev, libgl1-mesa-swx11-dev (> 6.5.1-0.4) to build dependencies * Added to Build-Depends: libtiff4-dev, libxaw7-dev * Standards-Version: 3.7.2 (no changes necessary) * debhelper 5 * use dpatch * Added license of new component RAxML to debian/copyright * Substituded ${Source-Version} by ${source:Version} resp. ${binary:Version} * debian/arb.menu: Applications/Science/Biology * move files from lib/* directly to /usr/lib/arb/lib instead of /usr/share/arb/lib and a bunch of symlinks * Set maintainer to Maintainer: Debian-Med Packaging Team * Added Portugese debconf translations (thanks to Miguel Figueiredo Closes: #341558 * Updated Czech debconf translations (thanks to Jakub Kasparec ) Closes: #356713, #392683 * Do not build molphy and symlink to molphy executables instead * New configuration file format for arb_tcp.dat * Added Vcs-Browser, Vcs-Svn * Moved Homepage from long description to tags field -- Andreas Tille Mon, 05 Nov 2007 18:17:32 +0100 arb (0.0.20050526-7) unstable; urgency=low * arb-common recommends arb * Added Build-Depends: g++ * Because there is no sign that this version shows the behaviour reported in #325640 against the former version and the bug reporter did not respond to any request I decide to close this bug. Feel free to reopen if it seems necessary. Clsoes: #325640 -- Andreas Tille Mon, 21 Nov 2005 14:09:01 +0100 arb (0.0.20050526-6) unstable; urgency=low * Added transfig to depends * Removed "Depends: arb" from arb-common to avoid circular dependencies Closes: #339861 * Added gcc 4.0.3 to supported compilers in Makefile -- Andreas Tille Wed, 9 Nov 2005 13:17:52 +0100 arb (0.0.20050526-5) unstable; urgency=low * Enable writing of large amounts of sequence files. (Thanks for the patch to Elmar Pruesse ) Closes: #333391 * Updated Swedish debconf template (Thanks to Daniel Nylander ) Closes: #332788 * Updated French debconf template (Thanks to Jean-Luc Coulon ) Closes: #333108 -- Andreas Tille Wed, 12 Oct 2005 09:25:15 +0200 arb (0.0.20050526-4) unstable; urgency=low * Included names.dat.template in arb-common:/var/lib/nas actually not only the file is missing but the directory of the file is also not found because a link to /var/lib/arb/nas is needed To enable a clean installation of the link the old empty directory has to be removed in a preinst script * Fixed location of arb nameserver in debian/conf/{arb_tcp,arb_ntree}.dat Closes: #332436 * Make sure that nameserver directory is accessible by members of group arb in postinst file * Changed debconf template to ask for arb users * Added warning to arb wrapper script if the user who starts arb is not yet member of group arb and thus not allowed to write to /var/lib/arb -- Andreas Tille Thu, 6 Oct 2005 21:38:12 +0200 arb (0.0.20050526-3) unstable; urgency=low * Added Swedish debconf templates translation (thanks to Daniel Nylander Closes: #330428 * Added ssh to dependencies because it is used in some scripts * Dropped last version number in Standards-Version (now: 3.6.2) -- Andreas Tille Wed, 28 Sep 2005 11:18:17 +0200 arb (0.0.20050526-2) unstable; urgency=low * Added explicite permission to distribute with Debian to debian/copyright * Fixed debian/rules + WINDOW/Makefile to ensure that libARB can be found in the build process (Many thanks to Petr Salinger ) * Reduced number of architectures to the set that features xviewg-dev -- Andreas Tille Thu, 8 Sep 2005 14:08:07 +0200 arb (0.0.20050526-1) unstable; urgency=low * New upstream version. * Added disclaimer from FTP-download directory to debian/arb.README.Debian and debian/copyright * Added parts of the disclaimer from FTP-download directory to debian/control * Patch for NAMES/names.cxx (Thanks to Petr Salinger ) -- Andreas Tille Tue, 30 Aug 2005 09:49:01 +0200 arb (0.0.20050506-3) unstable; urgency=low * Recommend: xfig * solved debconf | debconf-2.0 issue by ${misc:Depends} * debian/control: Homepage: http://www.arb-home.de/ * Renamed debian/po/cz.po to cs.po (Thanks to Denis Barbier ) Closes: #325062 * Depends: freeglut3-dev | libglu-dev * Build-Depends: libpng12-dev (Thanks to Petr Salinger ) * Some patches that where necessary for building with gcc 4.0.x (Thanks to Petr Salinger ) * arb-common: Depends: adduser * arb-common.config: Removed bashism -- Andreas Tille Fri, 26 Aug 2005 12:58:01 +0200 arb (0.0.20050506-2) unstable; urgency=low * Enable killing all arb processes in arb-kill * Standards-Version: 3.6.2.1 * menu items moved (no changes in packaging, just use new debhelper) * Czech debconf translation, thanks to Igor Jasa Closes: #318442 -- Andreas Tille Wed, 1 Jun 2005 13:15:04 +0200 arb (0.0.20050506-1) unstable; urgency=low * New upstream version * Adapted get-orig-source target to new directory layout * Added French debconf template Closes: #309222 -- Andreas Tille Mon, 30 May 2005 15:17:44 +0200 arb (0.0.20050318-1) unstable; urgency=low * New upstream snapshot * Added freeglut3-dev and libglew-dev Build-dependency * First official package uploaded to Debian Closes: #282037 -- Andreas Tille Thu, 10 Mar 2005 11:23:28 +0100 arb (0.0.20041206-1) unstable; urgency=low * New upstream snapshot * Reintegrate also arb-nas package because it is the main Arb application according to the author. It makes no sense to separate it in an extra package. -- Andreas Tille Mon, 06 Dec 2004 10:48:01 +0100 arb (0.0.20041112-4) unstable; urgency=low * Group arb which has rw-permissions to arb databases * Split configuration file into several pieces and megre them in postinst. This enables splitting into several independent packages because upstream uses a single config file * Script arb-add-pt-server enables users of group arb to add PT_SERVER entries to configuration files * Manage users of group arb via debconf -- Andreas Tille Tue, 23 Nov 2004 12:50:22 +0100 arb (0.0.20041112-3) unstable; urgency=low * Dropped package arb-extra and abr-server after discussing with the authors because it does not really make sense to split this from main package. * Enhanced package arb-nas * New package libarb with dynamic libraries -- Andreas Tille Fri, 19 Nov 2004 15:56:53 +0100 arb (0.0.20041112-2) unstable; urgency=low * Compile with libmotif-dev because liblesstif has trouble with some controls in the search inteface. * Moved some files to the server package. * Exclude arb/lib/BUGS from package because its irrelevant * Move arb/lib/help_html to doc package * Wrote placeholder manpage * Added lintian.overrides * Moved arb_tcp.dat to /etc/arb and set symlink -- Andreas Tille Tue, 16 Nov 2004 18:23:59 +0100 arb (0.0.20041112-1) unstable; urgency=low * Inoffcial test release. -- Andreas Tille Fri, 12 Nov 2004 13:15:16 +0100 debian/arb-common.README.debian0000644000000000000000000000055612214301210013310 0ustar ARB for Debian ============== ARB is restrictued to the architectures amd64 i386 kfreebsd-i386 kfreebsd-amd64 because the dependency RAxML is only available on these architectures (because it relays on SSE). This makes sense because ARB is most probably used on these architectures anyway. -- Andreas Tille Thu, 27 Jun 2013 14:52:57 +0200 debian/upstream0000644000000000000000000000365412214301210010743 0ustar Reference: - Author: Wolfgang Ludwig and Oliver Strunk and Ralf Westram and Lothar Richter and Harald Meier and Arno Buchner and Tina Lai and Susanne Steppi and Gangolf Jobb and Wolfram Forster and Igor Brettske and Stefan Gerber and Anton W Ginhart and Oliver Gross and Silke Grumann and Stefan Hermann and Ralf Jost and Andreas Konig and Thomas Liss and Ralph Lussmann and Michael May and Bjorn Nonhoff and Boris Reichel and Robert Strehlow and Alexandros Stamatakis and Norbert Stuckmann and Alexander Vilbig and Michael Lenke and Thomas Ludwig and Arndt Bode and Karl-Heinz Schleifer Title: "ARB: a software environment for sequence data" Journal: Nucl. Acids Res. Year: 2004 Volume: 32 Number: 4 Pages: 1363-1371 DOI: 10.1093/nar/gkh293 PMID: 14985472 URL: http://nar.oxfordjournals.org/content/32/4/1363.abstract eprint: http://nar.oxfordjournals.org/content/32/4/1363.full.pdf+html - Author: Yadhu Kumar and Ralf Westram and Sebastian Behrens and Bernhard Fuchs and Frank Oliver Glockner and Rudolf Amann and Harald Meier and Wolfgang Ludwig Title: Graphical representation of ribosomal RNA probe accessibility data using ARB software package Journal: BMC Bioinformatics Year: 2005 Volume: 21 Number: 6 Pages: 61 DOI: 10.1186/1471-2105-6-61 PMID: 15777482 URL: http://www.biomedcentral.com/1471-2105/6/61 eprint: http://www.biomedcentral.com/content/pdf/1471-2105-6-61.pdf - Author: Yadhu Kumar and Ralf Westram and Peter Kipfer and Harald Meier and Wolfgang Ludwig Title: Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package Journal: BMC Bioinformatics Year: 2006 Volume: 4 Number: 7 Pages: 240 DOI: 10.1186/1471-2105-7-240 PMID: 16672074 URL: http://www.biomedcentral.com/1471-2105/7/240/abstract eprint: http://www.biomedcentral.com/content/pdf/1471-2105-7-240.pdf debian/arb-common.manpages0000644000000000000000000000002712214301210012716 0ustar debian/bin/arb_clean.1 debian/arb-doc.doc-base0000644000000000000000000000107712214301210012063 0ustar Document: arb Title: ARB Manuals Author: Wolfgang Ludwig and Oliver Strunk Abstract: Integrated package for data handling and analysis The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. Section: Science/Biology Format: html Index: /usr/share/doc/arb/html/index.html Files: /usr/share/doc/arb/html/* debian/conf/0000755000000000000000000000000012214301210010075 5ustar debian/conf/arb_tcp_template.dat0000644000000000000000000000326112214301210014076 0ustar #******************* Syntax *********************************** # # [USER:]SERVER_ID HOST:IP_NR [programm args] # [USER:]SERVER_ID :SOCKETPATH [programm args] # [xxx] means optional field # all $(enviroment_variable) are replaced by the value of the 'enviroment_variable' # if host is localhost than it replaces by `hostname` # # Existing SERVER_IDs: # # ARB_DB_SERVER Your private database server. It is automatically started # ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server) # ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.) # n starts from 0 to max, no number can be excluded !!! # ARB_NAME_SERVER Generates short names for species # #***************************************************************** #*********** Private Servers (for each user) ****************** # # This is a local server, running on one machine. Each user has his own socket: # ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id # see programm $ARBHOME/SH/arb_clean to remove the sockets ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) # If you want to run programs on a workstation cluster, you have to assign your arbdb server # and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and # examine /etc/services whether this ip-id has not yet been allocated by another programm # smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' have to be started on 'myhost') # ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig # ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others #*********** Global Servers (for all users) ****************** # debian/conf/arb_pt_server.dat0000644000000000000000000000272612214301210013433 0ustar #*********** PT_SERVERS The server should run on the nfs server ****************** #******* You may add new pt_servers here: (numbers must be continues) ********* # FORMAT: # ARB_PT_SERVER localhost:303 arb_pt_server -D # where is a integer number increased by one according to the entry before # path_to_arb_database is the location of the database file # # The Debian packages contain a script arb-add-pt-server which enables each user # in group arb to add further PT_SERVERS. # # Under Debian we store the files under /var/lib/arb/pts but $(ARBHOME)/lib/pts # should work as well because it is symlinked # # The following database is shipped with the package arb-database # Further versions will add this in the postinst script but this is left # here for the process of beta testing. ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb # Examples: #ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/6rrns_sept99.arb #ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb #ARB_PT_SERVER3 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb #ARB_PT_SERVER4 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/16s_mw300WL_camp.arb #ARB_PT_SERVER5 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/3rrna_old.arb #ARB_PT_SERVER6 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/neu_08august5.arb #ARB_PT_SERVER7 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/3apr501.arb debian/conf/arb_ntree.dat0000644000000000000000000000032512214301210012530 0ustar #*********** Nameserver The server should run on the nfs server ****************** ## This is the Debian location for ARB name server ARB_NAME_SERVER localhost:3029 arb_name_server -d/var/lib/arb/nas/names.dat debian/conf/arb_tcp.dat0000644000000000000000000001117112214301210012202 0ustar #******************* Syntax *********************************** # # [USER:]SERVER_ID HOST:IP_NR [programm args] # [USER:]SERVER_ID :SOCKETPATH [programm args] # [xxx] means optional field # all $(enviroment_variable) are replaced by the value of the 'enviroment_variable'. # if host is localhost then it is replaced by the result of `hostname`. # # Specifying an username before the SERVER_ID makes the server user specific. # # This file is searched at several locations: # - in the current directory # - in the $(HOME) (=home directory of the current user) # - in $(ARBHOME)/lib # The first occurrance found is taken. # # Existing SERVER_IDs: # # ARB_DB_SERVER Your private database server. It is automatically started # ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server) # ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.) # n starts from 0 to max, no number can be excluded !!! # ARB_NAME_SERVER Generates short names for species (using 'acc') # ARB_NAME_SERVER_field Generates short names for species (using 'acc' and 'field') # #***************************************************************** # version of arb_tcp.dat ARB_TCP_DAT_VERSION 2 #*********** Private Servers (for each user) ****************** # # This is a local server, running on one machine. Each user has his own socket: # ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id # see programm $ARBHOME/SH/arb_clean to remove the sockets ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) # If you want to run programs on a workstation cluster, you have to assign your arbdb server # and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and # examine /etc/services whether this ip-id has not yet been allocated by another programm # smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' has to be started on 'myhost') # ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig # ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others #*********** Global Servers (for all users) ****************** # #*********** Nameserver The server should run on the nfs server ****************** # The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification # # You may define additional nameservers, using one additional field for identification. # The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'. ARB_NAME_SERVER localhost:3020 arb_name_server -d/var/lib/arb/nas/names.dat ARB_NAME_SERVER_START localhost:3021 arb_name_server -d/var/lib/arb/nas/names_start.dat -fstart #*********** PT_SERVERS The server should run on the nfs server ****************** #******* You may add new pt_servers here: (numbers must be continued) ********* # Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not # try to start/stop/update/... the server and will not check DB for existance. # To use such a PT-Server you'll have to start it manually on the remote host # # FORMAT: # ARB_PT_SERVER localhost:303 arb_pt_server -D # where is a integer number increased by one according to the entry before # path_to_arb_database is the location of the database file # # The Debian packages contain a script arb-add-pt-server which enables each user # in group arb to add further PT_SERVERS. # # Under Debian we store the files under /var/lib/arb/pts but $(ARBHOME)/lib/pts # should work as well because it is symlinked # # The following database is shipped with the package arb-database # Further versions will add this in the postinst script but this is left # here for the process of beta testing. ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb # Examples #ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/LSU_rRNA.arb #ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/SSU_rRNA.arb #ARB_PT_SERVER3 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb #ARB_PT_SERVER4 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb #ARB_PT_SERVER5 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/user3.arb #ARB_PT_SERVER6 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/user4.arb #ARB_PT_SERVER7 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/user5.arb #ARB_PT_SERVER8 localhost:3038 arb_pt_server -D$(ARBHOME)/lib/pts/user6.arb #ARB_PT_SERVER9 localhost:3039 arb_pt_server -D$(ARBHOME)/lib/pts/user7.arb #ARB_PT_SERVER10 localhost:3040 arb_pt_server -D$(ARBHOME)/lib/pts/user8.arb debian/conf/arb.conf0000644000000000000000000000105112214301210011505 0ustar # ARB_TEXTEDIT='xedit' ARB_TEXTEDIT=$EDITOR export ARB_TEXTEDIT ARB_XTERM='xterm -sl 1000 -sb' export ARB_XTERM ARB_XCMD='xterm -sl 1000 -sb -e' export ARB_XCMD # ARB_GS=ghostview ARB_GS=gv export ARB_GS ############################################################### ## Additional options for Debian GNU/Linux ############################################################### ## Navigation after firing up arb might be a little bit clumsy ## Thus you are able to set a directory for all users as default ## starting directory # ARBUSERDATA=${HOME}/arb debian/arb.install0000644000000000000000000000043712214301210011310 0ustar bin/[A-LN-Zabcd-z]* usr/lib/arb/bin debian/arb.xpm usr/share/arb debian/bin/arb usr/bin debian/bin/arb-add-pt-server usr/bin debian/bin/arb-kill usr/bin debian/conf/arb.conf etc/arb debian/conf/arb_tcp.dat etc/arb debian/arb-common.config0000644000000000000000000000420112214301210012366 0ustar #!/bin/sh set -e PROG=arb GROUP=${PROG} PROGUSERS="" DEBCONF_DEBUG=developer . /usr/share/debconf/confmodule db_version 2.0 ## Add group ${PROG} if not existent ## This returns the group including the members of the group which are needed later TESTGROUP=`getent group ${GROUP}` || true if [ -z "${TESTGROUP}" ] ; then addgroup --system "${GROUP}" >/dev/null # if the group was just created it can not have any users ... PROGUSERS="none" fi # store user info in TMPFILE TMPFILE=`tempfile` [ -s /etc/adduser.conf ] && . /etc/adduser.conf if [ _"$FIRST_UID" = _"" ] ; then FIRST_UID=1000 fi (IFS=":" while read user pass uid gid name rest ; do if [ "$uid" != "" ] ; then # in case NIS is used on the machine $uid remains # empty and breaks the following condition. if [ $uid -ge $FIRST_UID -a "$user" != "" ] ; then name=`echo $name | sed "s/,.*//"` echo "$user ($name)" >> ${TMPFILE} fi fi done < /etc/passwd ) # Login names of all users of the system as comma separated list USERS=`sort -u "${TMPFILE}" | tr '\n' ',' | sed 's/,/&\ /g' | sed 's/, *$//g'` # "login (Real Name)" of group "${PROG}" as comma separated list if [ "$PROGUSERS" != "none" ] ; then PROGUSERS=`echo "${TESTGROUP}" | sed "s/.*:\([^:]*\)/\1/" | tr ',' '\n'` # check whether the TESTGROUP contains any user or is just empty if [ _"$PROGUSERS" != _"" ] ; then TMPFILE2=`tempfile` for user in "${PROGUSERS}" ; do # add "|| true" because of -e option which would cause an exit otherwise grep -w "$user" "$TMPFILE" >> "$TMPFILE2" || true done mv "$TMPFILE2" "$TMPFILE" PROGUSERS=`sort -u "${TMPFILE}" | tr '\n' ',' | sed 's/,/&\ /g' | sed 's/, *$//g'` fi else PROGUSERS="" fi rm -rf "${TMPFILE}" # Check for system users who just belong to group ${PROG} if [ ! _"$PROGUSERS" = _"" ] ; then db_set ${GROUP}/group "$PROGUSERS" || true fi # Initialize List of Systemusers for debconf question db_subst ${GROUP}/group users "$USERS" || true db_get ${GROUP}/group || true db_input high ${GROUP}/group || true db_go || true debian/arb-common.postrm0000644000000000000000000000030312214301210012444 0ustar #!/bin/sh set -e # In case arb should be purged remove all stuff it might have dropped # in /var/lib if [ "$1" = "purge" ] && [ -d /var/lib/arb ]; then rm -rf /var/lib/arb fi #DEBHELPER# debian/arb.xpm0000644000000000000000000000102612214301210010441 0ustar /* XPM */ static char * arb_xpm[] = { "31 13 2 1", " c None", ". c #000000", " .. ", " ... .. ", " .... .. ", " ..... .. ", " ...... ... ... ", " ... .. .... ..... ", " ... .. ...... ..... ", " ... .. .. ..", " ... .. .. ..", " ... .. ... ..", " ... .. .. ...", " ... .. .. ........ ", "... .. .. ...... "}; debian/po/0000755000000000000000000000000012214301210007566 5ustar debian/po/pt.po0000644000000000000000000000227212214301210010554 0ustar # translation of arb debconf to Portuguese # Copyright (C) 2009 The arb's copyright holder # This file is distributed under the same license as the arb package. # # 2005-11-13 - Marco Ferra (initial translation) # Américo Monteiro , 2009. msgid "" msgstr "" "Project-Id-Version: arb 0.0.20071207.1-6\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2009-02-19 18:54+0000\n" "Last-Translator: Américo Monteiro \n" "Language-Team: Portuguese \n" "Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: KBabel 1.11.4\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Utilizadores do arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Por favor escolha da lista de utilizadores não-privilegiados do sistema, " "aqueles que terão permissão de correr o ${pkg}." debian/po/sv.po0000644000000000000000000000242712214301210010563 0ustar # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans # Developers do not need to manually edit POT or PO files. # , fuzzy # # msgid "" msgstr "" "Project-Id-Version: arb 0.0.20050526-2\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2005-10-09 18:16+0200\n" "Last-Translator: Daniel Nylander \n" "Language-Team: Swedish \n" "Language: sv\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=iso-8859-1\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Arb anvndare:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Vlj i listan av opriviligerade anvndare p systemet, de som ska tilltas " "att kra ${pkg}." debian/po/pt_BR.po0000644000000000000000000000217112214301210011135 0ustar # arb Brazilian Portuguese debconf template translation. # Copyright (C) 2010 arb's COPYRIGHT HOLDER # This file is distributed under the same license as the arb package. # Gustavo Jordan , 2010. # # msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2010-09-05 22:19-0300\n" "Last-Translator: Gustavo Jordan \n" "Language-Team: Brazilian Portuguese \n" "Language: pt_BR\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "pt_BR utf-8\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Usuários arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Por favor escolha, entre a lista de todos os usuários sem privilégios no " "sistema, aqueles que poderão executar ${pkg}." debian/po/nl.po0000644000000000000000000000206712214301210010544 0ustar # Dutch translation of arb debconf templates. # Copyright (C) 2012 THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the arb package. # Jeroen Schot , 2012. # msgid "" msgstr "" "Project-Id-Version: arb 5.3-2\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2012-01-05 16:31+0100\n" "Last-Translator: Jeroen Schot \n" "Language-Team: Debian l10n Dutch \n" "Language: nl\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Gebruikers van arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Geef in lijst van alle normale gebruikers van het systeem aan welke ${pkg} " "mogen uitvoeren." debian/po/sk.po0000644000000000000000000000237712214301210010554 0ustar # Slovak translations for arb package # Slovenské preklady pre balík arb. # Copyright (C) 2012 THE arb'S COPYRIGHT HOLDER # This file is distributed under the same license as the arb package. # Automatically generated, 2012. # Slavko , 2012. # msgid "" msgstr "" "Project-Id-Version: arb 5.3-4\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2012-08-30 21:34+0200\n" "Last-Translator: Slavko \n" "Language-Team: slovenčina \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Language: sk\n" "Plural-Forms: nplurals=3; plural=(n==1) ? 0 : (n>=2 && n<=4) ? 1 : 2;\n" "X-POFile-SpellExtra: arb pkg neprivilegovaných\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Používatelia arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Prosím, vyberte zo zoznamu všetkých neprivilegovaných používateľov systému " "tých, ktorým bude povolené spúšťanie ${pkg}." debian/po/it.po0000644000000000000000000000266112214301210010547 0ustar # translation of arb_0.0.20050526-7_cs.po to czech # # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans # # Developers do not need to manually edit POT or PO files. # #, fuzzy msgid "" msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2008-01-27 19:58+0100\n" "Last-Translator: David Paleino \n" "Language-Team: Italian \n" "Language: it\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Utente Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Per favore scegli, tra l'elenco di tutti gli utenti non privilegiati del " "sistema, quelli che avranno diritto ad eseguire ${pkg}." debian/po/es.po0000644000000000000000000000354112214301210010540 0ustar # arb po-debconf translation to Spanish # Copyright (C) 2010 Software in the Public Interest # This file is distributed under the same license as the arb package. # # Changes: # - Initial translation # Francisco Javier Cuadrado # # Traductores, si no conocen el formato PO, merece la pena leer la # documentación de gettext, especialmente las secciones dedicadas a este # formato, por ejemplo ejecutando: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Equipo de traducción al español, por favor lean antes de traducir # los siguientes documentos: # # - El proyecto de traducción de Debian al español # http://www.debian.org/intl/spanish/ # especialmente las notas y normas de traducción en # http://www.debian.org/intl/spanish/notas # # - La guía de traducción de po's de debconf: # /usr/share/doc/po-debconf/README-trans # o http://www.debian.org/intl/l10n/po-debconf/README-trans # msgid "" msgstr "" "Project-Id-Version: arb 0.0.20071207.1-7\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2010-03-05 09:00+0100\n" "Last-Translator: Francisco Javier Cuadrado \n" "Language-Team: Debian l10n Spanish \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Usuarios de arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Escoja de entre la lista de todos los usuarios sin privilegios del sistema, " "aquellos que podrán ejecutar ${pkg}." debian/po/POTFILES.in0000644000000000000000000000005712214301210011345 0ustar [type: gettext/rfc822deb] arb-common.templates debian/po/vi.po0000644000000000000000000000215112214301210010543 0ustar # Vietnamese translation for ARB. # Copyright © 2010 Free Software Foundation, Inc. # Clytie Siddall , 2010. # msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2010-04-01 00:16+0930\n" "Last-Translator: Clytie Siddall \n" "Language-Team: Vietnamese \n" "Language: vi\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" "X-Generator: LocFactoryEditor 1.8\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Người dùng Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Trong danh sách tất cả các người dùng hệ thống mà không có quyền đặc biệt, " "hãy chọn mỗi người dùng nên có quyền chạy ${pkg}." debian/po/ru.po0000644000000000000000000000247212214301210010561 0ustar # translation of ru.po to Russian # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # # Yuri Kozlov , 2009. msgid "" msgstr "" "Project-Id-Version: arb 0.0.20071207.1-5\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2009-01-10 11:24+0300\n" "Last-Translator: Yuri Kozlov \n" "Language-Team: Russian \n" "Language: ru\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: KBabel 1.11.4\n" "Plural-Forms: nplurals=3; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && n" "%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2);\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Пользователи Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Выберите всех непривилегированных пользователей системы из списка, которым " "будет разрешено запускать ${pkg}." debian/po/gl.po0000644000000000000000000000210112214301210010522 0ustar # Copyright (C) 2009 Marce Villarino # This file is distributed under the same license as the arb package. # # Marce Villarino , 2009. msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2009-07-19 11:25+0200\n" "Last-Translator: Marce Villarino \n" "Language-Team: Galician \n" "Language: gl\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Lokalize 0.3\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Usuarios de Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Escolla na lista de todos os usuarios sen privilexios do sistema, aqueles a " "quen se lles permitirá executar ${pkg}." debian/po/fi.po0000644000000000000000000000204212214301210010522 0ustar # Copyright (C) 2009 # This file is distributed under the same license as the arb package. # # Esko Arajärvi , 2009. msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2009-07-10 20:54+0300\n" "Last-Translator: Esko Arajärvi \n" "Language-Team: Finnish \n" "Language: fi\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Lokalize 0.3\n" "Plural-Forms: nplurals=2; plural=(n != 1);\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Arb-käyttäjät:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Valitse järjestelmän kaikkien tavallisten käyttäjien listalta ne, jotka " "saavat ajaa ohjelman ${pkg}." debian/po/ja.po0000644000000000000000000000220412214301210010516 0ustar # Copyright (C) 2009 Debian-Med Packaging Team # This file is distributed under the same license as the tipcutils package. # Hideki Yamane (Debian-JP) , 2009. # msgid "" msgstr "" "Project-Id-Version: arb 0.0.20071207.1-7\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2009-11-07 10:23+0900\n" "Last-Translator: Hideki Yamane (Debian-JP) \n" "Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "arb ユーザ:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "システムのすべての非特権ユーザの一覧から、${pkg} を動作させるのを許可するユー" "ザを選んでください。" debian/po/templates.pot0000644000000000000000000000157612214301210012321 0ustar # SOME DESCRIPTIVE TITLE. # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # FIRST AUTHOR , YEAR. # #, fuzzy msgid "" msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=CHARSET\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" debian/po/de.po0000644000000000000000000000255412214301210010524 0ustar # # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans # # Developers do not need to manually edit POT or PO files. # #, fuzzy msgid "" msgstr "" "Project-Id-Version: Arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2005-10-07 08:18+0100\n" "Last-Translator: Andreas Tille \n" "Language-Team: German \n" "Language: de\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=iso-8859-15\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Arb Nutzer:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Bitte whlen Sie aus der Liste aller nichtprivilegierten Nutzer des Systems " "all diejenigen aus, die ${pkg} nutzen drfen." debian/po/ca.po0000644000000000000000000000226612214301210010517 0ustar # translation of arb po to catalan # Catalan translation for arb package. # Copyright (C) 2007 Andreas Tille. # This file is distributed under the same license as the PACKAGE package. # Miguel Gea Milvaques , 2007. # Innocent De Marchi , 2011. # msgid "" msgstr "" "Project-Id-Version: 5.2-1\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2011-06-17 17:00+0100\n" "Last-Translator: Innocent De Marchi \n" "Language-Team: catalan \n" "X-Poedit-Language: Catalan\n" "X-Poedit-Country: SPAIN\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Usuaris Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Please choose, among the list of all unprivileged users of the system, those who will be allowed running ${pkg}." msgstr "Escolliu, d'aquesta llista de tots els usuaris del sistema sense privilegis, aquells als que es permetrà executar ${pkg}." debian/po/cs.po0000644000000000000000000000272312214301210010537 0ustar # translation of arb_0.0.20050526-7_cs.po to czech # # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans # # Developers do not need to manually edit POT or PO files. # # Jakub Kasparec , 2006. msgid "" msgstr "" "Project-Id-Version: arb_0.0.20050526-7_cs\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2006-10-12 21:23+0200\n" "Last-Translator: Jakub Kasparec \n" "Language-Team: czech \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: KBabel 1.11.4\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Uživatelé Arbu:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Prosím, zvolte, kteří z neprivilegovaných uživatelů systému budou moci " "spuštět ${pkg}." debian/po/fr.po0000644000000000000000000000252512214301210010541 0ustar # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans # Developers do not need to manually edit POT or PO files. # # msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2005-10-08 22:31+0200\n" "Last-Translator: Jean-Luc Coulon (f5ibh) \n" "Language-Team: French \n" "Language: fr\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=iso-8859-15\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Liste des utilisateurs d'Arb:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Veuillez choisir, parmi la liste des utilisateurs non privilgis du " "systme, ceux qui seront autoriss utiliser ${pkg}." debian/po/da.po0000644000000000000000000000201412214301210010507 0ustar # Dansih translation arb. # Copyright (C) 2010 arb & nedenstående oversættere. # This file is distributed under the same license as the arb package. # Joe Hansen , 2010. # msgid "" msgstr "" "Project-Id-Version: arb\n" "Report-Msgid-Bugs-To: arb@packages.debian.org\n" "POT-Creation-Date: 2009-03-20 08:21+0100\n" "PO-Revision-Date: 2010-06-02 17:30+01:00\n" "Last-Translator: Joe Hansen \n" "Language-Team: Danish \n" "Language: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "Arb users:" msgstr "Arb-brugere:" #. Type: multiselect #. Description #: ../arb-common.templates:1001 msgid "" "Please choose, among the list of all unprivileged users of the system, those " "who will be allowed running ${pkg}." msgstr "" "Vælg venligst, i listen over alle upriviligerede brugere af systemet, dem " "som må køre ${pkg}." debian/compat0000644000000000000000000000000212214301210010346 0ustar 9 debian/arb.README.debian0000644000000000000000000000613012214301210012014 0ustar Arb for DEBIAN -------------- Known bugs of arb are listed in the bug-tracker at http://bugs.arb-home.de/ Dependencies ------------ - Arb comes with its own version of Phylip. Because Phylip has its Debian package this is not build into arb package. Instead I replaced links to the apropriate locations. - Arb has its own version of FastDNAml which has also a separate Debian package. Here also symlinks to the Debian packaged version are used. - Arb makes also use of a patched Version of ReadSeq. The Arb version is identical with the latest C version (ReadSeq 2 is written from scratch in Java). The Arb-Verion is missing some patches, but has additional patches which make it incompatible with the Debian packaged version. I try to clarify this issue. - Arb has its own Version of tree-puzzle 5.0 which is completely identical with the Debian version. Just not compile it and set the apropriate links. - Arb contains a patched version of phyml which is lagging behind upstream releases of phyml. The latest version of phyml is available as Debian package as well and it is in the list of Suggested packages of Arb to enable you to compare the results. - The nameserver data are build in a separat package. The reason is that there are perhaps more recent packages available from http://download.arb-home.de/xtra/ So this package can be overridden by a separat package if necessary. - The internal copy of RAxML is also replaced by the Debian packaged version. Due to the fact that RAxML is using SSE and thus is only available on the architectures amd64 i386 kfreebsd-i386 kfreebsd-amd64 as a consequence also ARB is only build on these architectures This is most probably no restriction because ARB used on these architectures only anyway. Comments regarding the packaging -------------------------------- Config file: Under Debian GNU/Linux all configuration file have to be stored under /etc. Thus the config file is symlinked from /usr/lib/arb/lib/arb_tcp.dat to /etc/arb/arb_tcp.dat. User group arb: It has shown that arb users need to add their own PT_SERVER databases. To enable users to create such database files and insert this file into the config file a script arb-add-pt-server was written (see "man arb-add-pt-server"). Dynamic libraries: The dynamic libraries which are builded by the upstream Arb Makefile are moved from ${ARBHOME} to /usr/lib. Strangely enough these libraries issue a warninig of dpkg-shlibdeps: warning: format of libA*.so not recognized which results in a lintian error E: libarb: sharedobject-in-library-directory-not-actually-a-shlib usr/lib/libA*.so This was reportet upstream and is topic of further investigations. Potentially separate package Formerly arb_ntree was separated in an extra package which makes no real sense because it is the main Arb application. The only target for splitting would be PT-Server (binary bin/arb_pt_server - needs libraries+(arb_)gene_probe) -- Andreas Tille Thu, 27 Jun 2013 14:52:57 +0200 debian/patches/0000755000000000000000000000000012262753071010622 5ustar debian/patches/20_tmpfile_issue.patch0000644000000000000000000000361112214301210014772 0ustar Author: Andreas Tille Description: Proper use of tempfiles in scripts --- a/SH/arb_fastdnaml +++ b/SH/arb_fastdnaml @@ -1,5 +1,5 @@ #!/bin/sh -tmp=/tmp/arb_fdnaml_${USER}_$$ +tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX` mv infile $tmp nice -19 $1 < $tmp & sig=$! --- a/SH/dszmconnect.pl +++ b/SH/dszmconnect.pl @@ -20,7 +20,7 @@ use LWP::Simple; use HTTP::Request::Common qw(POST); use LWP::UserAgent; - +use File::Temp qw/ tempfile tempdir /; @@ -51,9 +51,12 @@ Last modified: Mon Sep 8 14:25:42 CEST "; +my $TMPOUT; +my $template = 'arbdsmz_XXXXXX'; +(undef, $TMPOUT) = tempfile($template, OPEN => 0); +$TMPOUT = $TMPOUT . ".html"; - -open (OUTPUT , "> /tmp/arbdsmz.html") or die "cannot open input file /tmp/arbdsmz.html"; +open (OUTPUT , "> $TMPOUT") or die "cannot open temporary input file $TMPOUT"; if (scalar(@ARGV) == 0) {print OUTPUT $errordocument; @@ -86,7 +89,10 @@ print STDERR "Searching for '$item2'\n"; $req_selection->content($selection_content); # Pass request to the user agent and get a response back - my $res_selection = $ua_selection -> request($req_selection, '/tmp/arbdsmz.htm'); + my $TMPUSEROUT; + (undef, $TMPUSEROUT) = tempfile($template, OPEN => 0); + $TMPUSEROUT = $TMPUSEROUT . ".htm"; + my $res_selection = $ua_selection -> request($req_selection, $TMPUSEROUT); @@ -95,7 +101,7 @@ print STDERR "Searching for '$item2'\n"; else {die "Bad luck this time, request failed\n";}; -open (INPUT , "< /tmp/arbdsmz.htm") or die "cannot open input file /tmp/arbdsmz.htm"; +open (INPUT , "< $TMPUSEROUT") or die "cannot open input file $TMPUSEROUT"; my $htmlcontent; @@ -111,7 +117,7 @@ $htmlcontent =~ s{HREF=[^"]}{HREF=http:/ print OUTPUT $htmlcontent ; -#exec ('netscape', '/tmp/arbdsmz.html'); -print "file:///tmp/arbdsmz.html"; +#exec ('netscape', $TMPOUT); +print "file://" . $TMPOUT; ##print "$htmlcontent\n"; debian/patches/40_add_libGLU.patch0000644000000000000000000000112512214301210014050 0ustar Author: Andreas Tille Description: Add missing libGLU --- a/Makefile +++ b/Makefile @@ -747,7 +747,7 @@ $(EDIT4): $(ARCHS_EDIT4:.a=.dummy) share @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) || ( \ echo Link $@ ; \ echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4)" ; \ - $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4) \ + $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) -lGLU $(LIBS_EDIT4) \ ) #*********************************** arb_pgt ************************************** debian/patches/60_use_debian_packaged_raxml.patch0000644000000000000000000000110112214301210017236 0ustar Author: Andreas Tille Description: Do not build raxml because we use Debian packaged version --- a/GDE/Makefile +++ b/GDE/Makefile @@ -3,7 +3,6 @@ ARCHS_ALL = \ CLUSTAL/CLUSTAL.dummy \ SUPPORT/SUPPORT.dummy \ AxML/AxML.dummy \ - RAxML/RAxML.dummy \ PHYML/PHYML.dummy \ # -------------------------------------------------------------------------------- @@ -15,6 +14,7 @@ ARCHS_ALL = \ ARCHS_NON_DEBIAN = \ CLUSTALW/CLUSTALW.dummy \ PHYLIP/PHYLIP.dummy \ + RAxML/RAxML.dummy \ TREEPUZZLE/TREEPUZZLE.dummy \ FASTDNAML/FASTDNAML.dummy \ debian/patches/hardening.patch0000644000000000000000000000100212247566401013575 0ustar Author: Andreas Tille Last-Update: Wed, 04 Dec 2013 09:24:14 +0100 Description: Propagate hardening options --- a/Makefile +++ b/Makefile @@ -107,7 +107,7 @@ ifeq ($(DEBUG),0) cflags := -O4# compiler flags (C and C++) ifndef DARWIN ifdef DEBIAN - lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib # linker flags + lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib $(LDFLAGS) # linker flags # remark: --strip-all option breaks g++ 4.6 and it's unwanted anyway else lflags += -O99# linker flags debian/patches/30_Makefile_main0000644000000000000000000000402612214301210013547 0ustar Author: Andreas Tille Date: Thu, 26 Jul 2012 12:15:21 +0200 Description: Some adaptations to Debian * Enable building with Debian default compiler * Enable fixing rpath issue when build under Debian * Fix X11 path * Enable propagation of hardening flags --- a/Makefile +++ b/Makefile @@ -67,8 +67,9 @@ ALLOWED_GCC_4xx_VERSIONS=\ 4.2.0 4.2.1 4.2.3 4.2.4 \ 4.3.1 4.3.2 4.3.3 \ 4.4.1 4.4.3 \ - 4.6.1 \ - 4.7.1 + 4.6.1 4.6.2 4.6.3 \ + 4.7.1 4.7.2 4.7.3 \ + 4.8.0 4.8.1 4.8.2 4.8.3 ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS) @@ -105,7 +106,12 @@ ifeq ($(DEBUG),0) dflags := -DNDEBUG# defines cflags := -O4# compiler flags (C and C++) ifndef DARWIN - lflags += -O99# linker flags + ifdef DEBIAN + lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib # linker flags + # remark: --strip-all option breaks g++ 4.6 and it's unwanted anyway + else + lflags += -O99# linker flags + endif endif endif @@ -208,7 +214,7 @@ cflags += -fPIC #---------------------- X11 location -ifdef DARWIN +ifdef DEBIAN XHOME:=$(PREFIX) else XHOME:=/usr/X11R6 @@ -285,9 +291,9 @@ endif # (instead define variables above) # ------------------------------------------------------------------------- -cflags += -W -Wall $(dflags) $(extended_warnings) $(cdynamic) +cflags += $(CFLAGS) -W -Wall $(dflags) $(extended_warnings) $(cdynamic) -cppflags := $(extended_cpp_warnings) +cppflags := $(extended_cpp_warnings) $(CPPFLAGS) ifeq ($(DEVELOPER),RALF) HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)` @@ -304,7 +310,7 @@ CPP := $(GPP) $(cppflags)# compile C++ ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs) CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs) -LINK_STATIC_LIB := ld $(lflags) $(ldynamic) -r -o# link static lib +LINK_STATIC_LIB := ld -rpath=/usr/lib/arb/lib -z relro -r -o# link static lib LINK_EXECUTABLE := $(GPP) $(lflags) $(cdynamic) -o# link executable (c++) ifeq ($(LINK_STATIC),1) debian/patches/50_fix_gcc-4.8.patch0000644000000000000000000000175512214301210014045 0ustar Author: Andreas Tille Description: Fix some gcc-4.8 issues --- a/GDE/SUPPORT/varpos.c +++ b/GDE/SUPPORT/varpos.c @@ -1,3 +1,4 @@ +#include "stdlib.h" #include "Flatio.c" #define MAX(a,b) ((a)>(b)?(a):(b)) --- a/GDE/AxML/axml.c +++ b/GDE/AxML/axml.c @@ -9,6 +9,8 @@ #include #include #include +#include +#include double accTime = 0.0; double globTime = 0.0; struct timeval ttime; --- a/GDE/AxML/axml.h +++ b/GDE/AxML/axml.h @@ -266,12 +266,6 @@ typedef struct { void exit(); -#if ANSI || MALLOC_VOID - void *malloc(); -#else - char *malloc(); -#endif - #define Malloc(x) malloc((unsigned) (x)) /* BSD */ /* #define Malloc(x) malloc((size_t) (x)) */ /* System V */ --- a/GDE/AxML/Makefile +++ b/GDE/AxML/Makefile @@ -33,7 +33,7 @@ endif all : $(TARGET) $(TARGET) : $(OBJECTS) - $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) + $(CC) $(CFLAGS) -o $@ $< -lm .c.o: $(CC) $(CFLAGS) -c -o $@ $< debian/patches/30_phyml0000644000000000000000000000060712214301210012160 0ustar Author: Andreas Tille Description: Prevent static linking of phyml --- a/GDE/PHYML/Makefile +++ b/GDE/PHYML/Makefile @@ -13,7 +13,8 @@ ifndef ARB # original compilation CC = gcc #cc -CFLAGS = -O4 -fomit-frame-pointer -Wall -static +CFLAGS = -O4 -fomit-frame-pointer -Wall +# -static # CFLAGS = -Wall # CFLAGS = -g -Wall # CFLAGS = -pg -Wall -fprofile-arcs -static debian/patches/gl-and-motif-headers.diff0000644000000000000000000000061612262753052015345 0ustar --- a/RNA3D/RNA3D_GlobalHeader.hxx +++ b/RNA3D/RNA3D_GlobalHeader.hxx @@ -47,4 +47,15 @@ #endif // OPEN_GL_WAY_TO_INCLUDE == 3 // ------------------------------ +#include +#ifdef GLAPI +# define SAVED_GLAPI GLAPI +# undef GLAPI +#endif +#define GLAPI extern #include +#undef GLAPI +#ifdef SAVED_GLAPI +# define GLAPI SAVED_GLAPI +# undef SAVED_GLAPI +#endif debian/patches/20_config.makefiles0000644000000000000000000000234012214301210014226 0ustar Author: Andreas Tille Description: Set basic makefile configuration variables --- /dev/null +++ b/config.makefile @@ -0,0 +1,27 @@ +# -------------------------------------------------------------------------------- +# If this file is named config.makefile.template then copy it to config.makefile +# DO NOT EDIT config.makefile.template +# -------------------------------------------------------------------------------- + +# Enter your name (upper case, no spaces) here, to enable '#ifdef DEVEL_YOURNAME #endif' sections +DEVELOPER=ANY + +DEBUG=0# build with debug information +DEBUG_GRAPHICS = 0# force instant graphic update +# SEER = 1 +OPENGL=1 +# ARB_64=0# compile on 64 bit machine (has no effect yet) +ARB_64 := $(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH_BITS` -eq 64 ] ; then echo 1 ; else echo 0 ; fi) + +# -------------------------------------------------------------------------------- +# target machine section +# [Note: Uncomment one section, depending on your machine type and compiler options] + +# ********* LINUX / gcc g++ / static ******** +MACH = LINUX# Linux g++ and gcc +LINUX = 1 +ECGS = 1# use GCC? (always 1 for LINUX) + +# ******** Debian GNU/Linux and (K)Ubuntu system ******** +DEBIAN = 1 + debian/patches/50_build_naligner.patch0000644000000000000000000000062212214301210015102 0ustar Author: Andreas Tille Description: Some build flags were simply not propagated in $(CFLAGS) - use $(cflags) --- a/NALIGNER/Makefile +++ b/NALIGNER/Makefile @@ -22,7 +22,7 @@ $(MAIN): $(CPP_OBJECTS) $(LINK_STATIC_LIB) $(MAIN) $(CPP_OBJECTS) .cxx.o: - $(CPP) $(CFLAGS) -c -o $@ $< $(CPPINCLUDES) + $(CPP) $(cflags) -c -o $@ $< $(CPPINCLUDES) clean: rm -f $(CPP_OBJECTS) *.a debian/patches/series0000644000000000000000000000037412262753071012043 0ustar 30_phyml 20_config.makefiles 30_Makefile_main 20_Makefiles 20_tmpfile_issue.patch tmpfile_CVE-2008-5378.patch 40_add_libGLU.patch 50_build_naligner.patch 50_fix_gcc-4.8.patch 60_use_debian_packaged_raxml.patch hardening.patch gl-and-motif-headers.diff debian/patches/tmpfile_CVE-2008-5378.patch0000644000000000000000000000407312214301210014754 0ustar BugClosed: http://bugs.debian.org/508942 Description: This patch fixes tmpfile issues reported in CVE-2008-5378 --- a/SH/arb_fastdnaml +++ b/SH/arb_fastdnaml @@ -1,9 +1,10 @@ #!/bin/sh tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX` +pidfile=`mktemp -p /tmp foo_${USER}_${PPID}_XXXXXX` mv infile $tmp nice -19 $1 < $tmp & sig=$! -/bin/echo "$sig $$ \c" >>/tmp/arb_pids_${USER}_${ARB_PID} +/bin/echo "$sig $$ \c" >>"$pidfile" wait # echo $tmp not deleted for debugging purposes rm -f $tmp --- a/SH/arb_clean +++ b/SH/arb_clean @@ -9,9 +9,14 @@ else pidfiles=/tmp/arb_pids_${USER}_${ARB_PID} fi -if [ "\"X$pidfiles\"" != "X" ]; then +# Make sure files to remove are no symbolic links +if [ "\"X$pidfiles\"" != "X" -a -f "$pidfiles" ]; then kill -9 `cat $pidfiles` >/dev/null 2>&1 rm -f $pidfiles fi -rm -f /tmp/arb_*_${USER}_${ARB_PID}* +for pidfile in /tmp/arb_*_${USER}_${ARB_PID}* ; do + if [ -f "$pidfile" ] ; then + rm -f "$pidfile" + fi +done --- a/SH/arb_panic +++ b/SH/arb_panic @@ -21,7 +21,9 @@ echo " There may be more than one datab echo " --------------------------------" for i in $chooser ; do - /bin/echo " - >" `ls $i` "<"; + if [ ! -L "$i" ] ; then + /bin/echo " - >" `ls $i` "<"; + fi done echo " --------------------------------" @@ -29,19 +31,21 @@ seperator echo "Please choose one line and enter the rightmost number" read ARB_PID -if [ ! -f /tmp/arb_pids_${USER}_${ARB_PID} ]; then - err "Incorrect Choice" -fi +for arbpid in /tmp/arb_pids_${USER}_${ARB_PID}* ; do + if [ ! -f "$arbpid" ]; then + err "Incorrect Choice" + fi +done seperator echo "Please enter full path (to save DB):" read FILE -panicfile="/tmp/arb_panic_${USER}_${ARB_PID}" +panicfile=`mktemp -p /tmp arb_panic_${USER}_${ARB_PID}_XXXXXX` rm -f $panicfile echo "$FILE" >$panicfile ok=false -for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}`; do +for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}*`; do echo "[Sending SIGHUP to pid $i]" if kill -HUP $i 2>/dev/null; then ok=true debian/patches/20_Makefiles0000644000000000000000000000762012214301210012730 0ustar Author: Andreas Tille Description: Fix various clean targets --- a/ARBDB2/Makefile +++ b/ARBDB2/Makefile @@ -1,7 +1,11 @@ # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben .SUFFIXES: .o .c .depend -include AD_MOBJECTS.h +HeaderFile = AD_MOBJECTS.h +CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi) +ifeq ($(CheckHEADER),1) + include $(HeaderFile) +endif ACC_OBJECTS = $(GB_O) $(GB_T) $(GB_X) --- a/ARBDBS/Makefile +++ b/ARBDBS/Makefile @@ -1,7 +1,11 @@ # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben .SUFFIXES: .o .c .cxx .depend -include AD_MOBJECTS.h +HeaderFile = AD_MOBJECTS.h +CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi) +ifeq ($(CheckHEADER),1) + include $(HeaderFile) +endif OBJECTS = $(GB_O) $(GB_T) $(GB_PP) $(GB_X) --- a/NAMES_COM/Makefile +++ b/NAMES_COM/Makefile @@ -18,7 +18,7 @@ CLIENTCOMPILER = $(COMPILER) AISC_COMPILER=../MAKEBIN/aisc AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) -include AISC/export2sub +include $(ARBHOME)/AISC_COM//AISC/export2sub server.a: $(MAIN_SOURCE) $(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS) @$(MAKE) -r -f AISC/Makefile @@ -27,7 +27,7 @@ depends: @$(MAKE) -r -f AISC/Makefile pregenerate clean: - @$(MAKE) -r -f AISC/Makefile clean + @$(MAKE) -r -f ../AISC/Makefile clean # DO NOT DELETE --- a/PROBE_COM/Makefile +++ b/PROBE_COM/Makefile @@ -18,7 +18,7 @@ CLIENTCOMPILER := $(COMPILER) AISC_COMPILER=../MAKEBIN/aisc AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) -include AISC/export2sub +include $(ARBHOME)/AISC_COM//AISC/export2sub server.a: $(MAIN_SOURCE) $(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS) @$(MAKE) -r -f AISC/Makefile @@ -27,7 +27,7 @@ depends: @$(MAKE) -r -f AISC/Makefile pregenerate clean: - @$(MAKE) -r -f AISC/Makefile clean + @$(MAKE) -r -f ../AISC/Makefile clean # DO NOT DELETE --- a/GENOM_IMPORT/Makefile +++ b/GENOM_IMPORT/Makefile @@ -30,12 +30,12 @@ $(MAIN): $(CPP_OBJECTS) $(ACC) $(cflags) -c $< $(CPPINCLUDES) clean: - -rm *.o - -rm *.a - -rm *.bak - -rm *~ - -rm *# - -rm *\% + -rm -f *.o + -rm -f *.a + -rm -f *.bak + -rm -f *~ + -rm -f *# + -rm -f *\% #.IGNORE: # clean --- a/HELP_SOURCE/Makefile +++ b/HELP_SOURCE/Makefile @@ -151,7 +151,7 @@ $(HLP_DEST)/%.pdf.gz : $(HLP_SOURCE)/%.p # -------------------------------------------------------------------------------- delzerohtml: - -find $(HTML_LOCATION) -name "*.html" -size -1 -exec rm {} \; + -if [ -d $(HTML_LOCATION) ] ; then find $(HTML_LOCATION) -name "*.html" -size -1 -exec rm {} \; ; fi date : $(MAKE) date.xsl.tmp --- a/GDEHELP/Makefile.helpfiles +++ b/GDEHELP/Makefile.helpfiles @@ -2,9 +2,9 @@ .SUFFIXES: .doc .help .html -# GENHELPDEST, GENDOCDEST and HELPFILELIST are passed from 'Makefile' +# GENHELPDEST, GENDOCDEST and HELP_NAMES are passed from 'Makefile' -HELP_NAMES=$(shell cat $(HELPFILELIST)) +# HELP_NAMES=$(shell cat $(HELPFILELIST)) HELP_TARGETS=$(addprefix $(GENHELPDEST)/,$(HELP_NAMES)) HELP_PLAIN=./HELP_PLAIN HELP_WRITTEN=./HELP_WRITTEN --- a/GDEHELP/Makefile +++ b/GDEHELP/Makefile @@ -47,11 +47,19 @@ save: tar cvf - MENUS ARB_GDEmenus* |gzip >`date '+arbgdemnus_%d_%m_%y.tar.gz'` clean: - rm -f $(GENMENUS) $(MENUS) $(HELPFILELIST) - @$(MAKE) -f Makefile.helpfiles \ - "GENHELPDEST=$(GENHELPDEST)" \ - "GENDOCDEST=$(GENDOCDEST)" \ - "HELPFILELIST=$(HELPFILELIST)" \ - clean - rm -f $(GENMENUS) $(MENUS) $(HELPFILELIST) + rm -f $(GENMENUS) $(MENUS) + @if [ -e $(HELPFILELIST) ] ; then \ + $(MAKE) -f Makefile.helpfiles \ + "GENHELPDEST=$(GENHELPDEST)" \ + "GENDOCDEST=$(GENDOCDEST)" \ + "HELPFILELIST=$(HELPFILELIST)" \ + clean ; \ + else \ + $(MAKE) -f Makefile.helpfiles \ + "GENHELPDEST=$(GENHELPDEST)" \ + "GENDOCDEST=$(GENDOCDEST)" \ + "HELPFILELIST=$(HELPFILELIST)" \ + clean ; \ + fi + rm -f $(HELPFILELIST) debian/arb.manpages0000644000000000000000000000010612214301210011426 0ustar debian/bin/arb.1 debian/bin/arb-kill.1 debian/bin/arb-add-pt-server.1 debian/control0000644000000000000000000001042512247566026010605 0ustar Source: arb Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: non-free/science XS-Autobuild: yes Priority: optional Build-Depends: chrpath, debhelper (>= 9), freeglut3-dev | libglu-dev, libbio-perl-perl, libglew-dev, libglw1-mesa-dev, libglu1-mesa-dev, libmotif-dev, libpng-dev, libtiff-dev, libxaw7-dev, libxml2-utils, libxpm-dev, lynx, time, perl-doc, xsltproc, xutils-dev Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/arb/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/arb/trunk/ Homepage: http://www.arb-home.de/ Package: arb Architecture: amd64 i386 kfreebsd-i386 kfreebsd-amd64 Depends: arb-common (= ${source:Version}), fastdnaml, libarb (= ${binary:Version}), openssh-client, phylip, raxml, readseq, transfig, tree-puzzle, ${misc:Depends}, ${shlibs:Depends} Recommends: bioperl, xfig Suggests: arb-database, gnuplot, gv, phyml Description: Integrated package for sequence database handling and analysis The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. . The ARB project (latin, "arbor"=tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation http://wwwbode.informatik.tu-muenchen.de/ of the Technical University of Munich. Package: libarb Architecture: amd64 i386 kfreebsd-i386 kfreebsd-amd64 Depends: ${misc:Depends}, ${shlibs:Depends} Recommends: arb Description: Integrated package for sequence database handling and analysis The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. . The ARB project (latin, "arbor"=tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation http://wwwbode.informatik.tu-muenchen.de/ of the Technical University of Munich. . This package contains the dynamic libraries which are used by arb. Package: arb-common Architecture: all Depends: adduser, arb-doc (= ${source:Version}), ghostscript | postscript-preview, gv | postscript-viewer, perl-modules, ${misc:Depends}, ${perl:Depends} Recommends: arb Description: Integrated package for sequence database handling and analysis (data+scripts) The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. . This package contains the architecture independent scripts of Arb. Package: arb-doc Architecture: all Section: non-free/doc Depends: ghostscript | postscript-preview, gv | postscript-viewer, ${misc:Depends} Suggests: arb Description: Integrated package for sequence database handling and analysis (docs) The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. . This package contains the documentation for the package arb. debian/arb-doc.lintian-overrides0000644000000000000000000000054112214301210014037 0ustar # While the arb-doc package in fact contains documentation # that can be read by itself it is a basic component of the # help system binary programm arb and needs to be installed # in any case if arb should be running. So the decision # to move arb-doc not into the doc section was done intentionally arb-doc: doc-package-should-be-section-doc arb-doc debian/arb-common.dirs0000644000000000000000000000006712214301210012070 0ustar usr/share/lintian/overrides usr/bin usr/share/doc/arb/ debian/arb-doc.links0000644000000000000000000000010612214301210011516 0ustar usr/share/doc/arb/html/manual.html usr/share/doc/arb/html/index.html debian/rules0000755000000000000000000001107312214301210010232 0ustar #!/usr/bin/make -f # debian/rules for arb using quilt # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') pkgcom=$(pkg)-common pkgdoc=$(pkg)-doc common=debian/$(pkgcom) ARBHOME=$(CURDIR) BITARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS) ifeq ($(BITARCH),64) ARB_64:=1 else ARB_64:=0 endif %: dh $@ override_dh_auto_build: mkdir -p LIBLINK MAKEBIN lib/help export LC_ALL=C ; \ export PATH=$(ARBHOME)/bin:$${PATH} ; \ export LD_LIBRARY_PATH=$(ARBHOME)/lib:$${LD_LIBRARY_PATH} && \ $(MAKE) DEBIAN=1 ARBHOME=$(ARBHOME) ARB_64=$(ARB_64) \ CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)" -lm \ all && \ export LD_LIBRARY_PATH=$(ARBHOME)/lib:$${LD_LIBRARY_PATH} && \ $(MAKE) DEBIAN=1 ARBHOME=$(ARBHOME) ARB_64=$(ARB_64) \ CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)" -lm \ arbxtras export LD_LIBRARY_PATH=$(ARBHOME)/lib:$${LD_LIBRARY_PATH}; \ cd HELP_SOURCE; $(MAKE) ARBHOME=$(ARBHOME) html #Ensure arb_edit4 was actually built ls bin/arb_edit4 # Remove links inside these directories because Makefile does not really clean # these directories DIRSTOREMOVELINKS=AWT ARBDBS ARBDB2 EDIT4 LIBLINK MAKEBIN NALIGNER NAMES_COM ORS_COM PROBE PROBE_COM PROBE_SERVER TOOLS bin lib/inputMasks lib/help # The following subdirectorys where created at compile time in some directories # but will not be removed by clean target SUBDIRSTOREMOVE=GENC GENH O # Sometimes clean target does not work as expected. Try to clean some dirs manually DIRSTOCLEAN=AISC AISC_MKPTPS SOURCE_TOOLS RemoveFromSourceAndBuild=PERL2ARB/Makefile PERL2ARB/ARB.c HELP_SOURCE/date.xsl \ lib/arb_tcp.dat lib/ARB.pm \ *.last_gcc TEMPLATES/arb_build.h \ GDE/MOLPHY/prot_tml.h \ PERL2ARB/perlmain.c \ PERL2ARB/ARB.bs PERL_SCRIPTS/test/test.stamp PERL2ARB/MYMETA.yml FILESTOREMOVE=libXm.so.3 NALIGNER/NALIGNER.com lib/nas/names.dat $(RemoveFromSourceAndBuild) DIRSTOREMOVE=INCLUDE HELP_SOURCE/Xml lib/help lib/help_html PERL5 lib/perl5 PROBE_SERVER/bin PERL2ARB/blib/man3 PROBE_SET/bin DirsToKeepOnlyMAKEFILE=bin override_dh_auto_clean: # Make does only work if config.makefile exists which is only the # case when quilt has installed the patches. So there is neither # a need nor the expection of success if config.makefile is missing [ ! -f config.makefile ] || $(MAKE) DEBIAN=1 ARBHOME=$(ARBHOME) clean # fix broken clean process find . -type f -name "*.a" -delete find . -type f -name "*.o" -delete find . -type f -name "*.so" -delete rm -f `find bin -name "arb*" | grep -v ".pl$$"` rm -f `find $(DIRSTOREMOVELINKS) -type l` rm -f `find . -type f -name ".depends"` for dir in $(SUBDIRSTOREMOVE) ; do \ rm -rf `find . -name $${dir} -type d` ; \ done rm -f `find $(DirsToKeepOnlyMAKEFILE) -maxdepth 1 -type f | grep -v Makefile` rm -f `find PROBE_WEB/CLIENT -name \*.class -type f` rm -f `find PROBE_WEB/CLIENT -name \*.jar -type f` rm -f $(FILESTOREMOVE) rm -fr $(DIRSTOREMOVE) for dtc in $(DIRSTOCLEAN); do if [ -d $${dtc} ] ; then cd $${dtc}; make clean ; fi; done find . -name "*.stamp" -o -name "*.bs" -o -name ".exists" -delete override_dh_install: dh_install # remove files from arb package which are in arb-nas if [ -s debian/arb-nas.install ] ; then \ for arbfile in `sed 's?^bin/\([^[:space:]]\+\)[[:space:]]\+\(.\+\)?debian/$(pkg)/\2/\1?' debian/arb-nas.install | grep debian/$(arb)` ; do \ rm -f $${arbfile} ; \ done ; \ fi # the check is needed to make sure it will not fail when doing binary-arch only builds if [ -e debian/$(pkgcom)/usr/lib/arb/SH/arb_create_debian_conffile ] ; then \ # Move SH/README to docs \ cp -a SH/README debian/$(pkgcom)/usr/share/doc/arb/README_SH ; \ # Fix permission of scripts \ chmod a+x debian/$(pkgcom)/usr/lib/arb/SH/arb_create_debian_conffile ; \ chmod a+x debian/$(pkgcom)/usr/lib/arb/lib/macro.head ; \ fi # Man page is not really needed and throws just a lintian warning # mkdir `pwd`/debian/$(pkg)/usr/share/man/man3 # perldoc PERL2ARB/ARB.pm > `pwd`/debian/$(pkg)/usr/share/man/man3/ARB.3pm override_dh_strip: # Fix rpath issue (once libarb is installed) if [ -e debian/libarb/usr/lib/arb/lib/ARB.so ] ; then \ chrpath --delete debian/libarb/usr/lib/arb/lib/ARB.so ; \ fi dh_strip override_dh_shlibdeps: dh_shlibdeps -a -l debian/libarb/usr/lib override_dh_builddeb: dh_builddeb -- -Z xz # To update po files as recommended in po-debconf(7) debian/po/templates.pot: debian/arb-common.templates @debconf-updatepo debian/source/0000755000000000000000000000000012214301210010450 5ustar debian/source/format0000644000000000000000000000001412214301210011656 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000061112214301210011325 0ustar Remark: The Build could profit from a Build-Depends if this Module would be packaged for Debian http://search.cpan.org/~pevans/B-LintSubs-0.04/lib/B/LintSubs.pm This would prevent the following warning: You either lack S::LintSubs and/or Bio::TreeIO or the perl scripts are buggy. We continue anyway.. -- Andreas Tille Thu, 09 Feb 2012 13:44:22 +0100 debian/watch0000644000000000000000000000040712214301210010202 0ustar version=3 # opts="uversionmangle=s/_//g;s/^/0.0./" \ # http://download.arb-home.de/src/arbsrc_([[:digit:]].*)\.(?:tar\.gz|tar|tgz)$ opts="downloadurlmangle=s/$/arbsrc.tgz/,filenamemangle=s/\/$/.tgz/" \ http://download.arb-home.de/release/ arb_(\d+.*)/ debian/libarb.install0000644000000000000000000000004312214301210011770 0ustar lib/*.so usr/lib/arb/lib