[med-svn] r759 - in trunk/packages: . arb arb/trunk arb/trunk/debian arb/trunk/debian/bin arb/trunk/debian/conf arb/trunk/debian/patches arb/trunk/debian/po
tille at alioth.debian.org
tille at alioth.debian.org
Mon Nov 5 19:22:15 UTC 2007
Author: tille
Date: 2007-11-05 19:22:14 +0000 (Mon, 05 Nov 2007)
New Revision: 759
Added:
trunk/packages/arb/
trunk/packages/arb/trunk/
trunk/packages/arb/trunk/debian/
trunk/packages/arb/trunk/debian/About
trunk/packages/arb/trunk/debian/arb-common.README.debian
trunk/packages/arb/trunk/debian/arb-common.config
trunk/packages/arb/trunk/debian/arb-common.dirs
trunk/packages/arb/trunk/debian/arb-common.install
trunk/packages/arb/trunk/debian/arb-common.links
trunk/packages/arb/trunk/debian/arb-common.manpages
trunk/packages/arb/trunk/debian/arb-common.postinst
trunk/packages/arb/trunk/debian/arb-common.preinst
trunk/packages/arb/trunk/debian/arb-common.templates
trunk/packages/arb/trunk/debian/arb-doc.doc-base
trunk/packages/arb/trunk/debian/arb-doc.install
trunk/packages/arb/trunk/debian/arb-doc.links
trunk/packages/arb/trunk/debian/arb.README.debian
trunk/packages/arb/trunk/debian/arb.install
trunk/packages/arb/trunk/debian/arb.links
trunk/packages/arb/trunk/debian/arb.manpages
trunk/packages/arb/trunk/debian/arb.menu
trunk/packages/arb/trunk/debian/arb.postinst
trunk/packages/arb/trunk/debian/arb.xpm
trunk/packages/arb/trunk/debian/bin/
trunk/packages/arb/trunk/debian/bin/arb
trunk/packages/arb/trunk/debian/bin/arb-add-pt-server
trunk/packages/arb/trunk/debian/bin/arb-add-pt-server.1
trunk/packages/arb/trunk/debian/bin/arb-kill
trunk/packages/arb/trunk/debian/bin/arb-kill.1
trunk/packages/arb/trunk/debian/bin/arb.1
trunk/packages/arb/trunk/debian/bin/arb_clean.1
trunk/packages/arb/trunk/debian/bin/arb_create_debian_conffile
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/compat
trunk/packages/arb/trunk/debian/conf/
trunk/packages/arb/trunk/debian/conf/arb.conf
trunk/packages/arb/trunk/debian/conf/arb_ntree.dat
trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat
trunk/packages/arb/trunk/debian/conf/arb_tcp.dat
trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat
trunk/packages/arb/trunk/debian/control
trunk/packages/arb/trunk/debian/copyright
trunk/packages/arb/trunk/debian/get-orig-source
trunk/packages/arb/trunk/debian/libarb.install
trunk/packages/arb/trunk/debian/lintian.overrides
trunk/packages/arb/trunk/debian/patches/
trunk/packages/arb/trunk/debian/patches/00list
trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch
trunk/packages/arb/trunk/debian/patches/20_config.makefiles.dpatch
trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch
trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch
trunk/packages/arb/trunk/debian/po/
trunk/packages/arb/trunk/debian/po/POTFILES.in
trunk/packages/arb/trunk/debian/po/cs.po
trunk/packages/arb/trunk/debian/po/de.po
trunk/packages/arb/trunk/debian/po/fr.po
trunk/packages/arb/trunk/debian/po/sv.po
trunk/packages/arb/trunk/debian/po/templates.pot
trunk/packages/arb/trunk/debian/rules
Log:
Added arb
Added: trunk/packages/arb/trunk/debian/About
===================================================================
--- trunk/packages/arb/trunk/debian/About (rev 0)
+++ trunk/packages/arb/trunk/debian/About 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,40 @@
+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.
Added: trunk/packages/arb/trunk/debian/arb-common.README.debian
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.README.debian (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.README.debian 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+Please read the docs in /usr/share/doc/arb.
Added: trunk/packages/arb/trunk/debian/arb-common.config
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.config (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.config 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,75 @@
+#!/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
+ /usr/sbin/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 -ge $FIRST_UID ] ; then
+ if [ ! "$user" = "nobody" ] ; 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
Added: trunk/packages/arb/trunk/debian/arb-common.dirs
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.dirs (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.dirs 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,2 @@
+usr/share/lintian/overrides
+usr/bin
Added: trunk/packages/arb/trunk/debian/arb-common.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.install (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.install 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,21 @@
+GDEHELP/DATA_FILES usr/share/arb/GDEHELP
+GDEHELP/ARB_GDEmenus etc/arb
+PERL_SCRIPTS usr/share/arb
+SH usr/share/arb
+HELP_SOURCE/oldhelp/*.hlp usr/share/arb/HELP_SOURCE/oldhelp
+HELP_SOURCE/oldhelp/prompt usr/share/arb/HELP_SOURCE/oldhelp
+HELP_SOURCE/oldhelp/seer usr/share/arb/HELP_SOURCE/oldhelp
+lib/[d-gi-kmoqrt-z]* usr/share/arb/lib
+lib/pi* usr/share/arb/lib
+lib/s[a-tv-z]* usr/share/arb/lib
+lib/pts var/lib/arb
+lib/arb_default/* usr/share/arb/lib/arb_default
+lib/help usr/share/arb/lib
+lib/ARB.pm usr/share/arb/lib
+GDEHELP/HELP_GEN/* usr/share/arb/GDEHELP
+lib/config.Linux usr/share/arb/lib
+debian/bin/arb_create_debian_conffile usr/share/arb/SH
+lib/nas/names.dat* var/lib/arb/nas
+demo.arb usr/share/doc/arb/examples
+debian/About usr/share/doc/arb/
+lib/submit usr/share/doc/arb
Added: trunk/packages/arb/trunk/debian/arb-common.links
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.links (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.links 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,11 @@
+etc/arb/ARB_GDEmenus usr/share/arb/GDEHELP/ARB_GDEmenus
+usr/share/arb/GDEHELP usr/lib/arb/GDEHELP
+usr/share/arb/PERL_SCRIPTS usr/lib/arb/PERL_SCRIPTS
+usr/share/arb/SH usr/lib/arb/SH
+usr/share/arb/HELP_SOURCE usr/lib/arb/HELP_SOURCE
+usr/share/arb/lib usr/lib/arb/lib
+var/lib/arb/pts usr/share/arb/lib/pts
+var/lib/arb/nas usr/share/arb/lib/nas
+usr/share/arb/SH/arb_clean usr/bin/arb_clean
+usr/share/doc/arb/html usr/share/arb/lib/html_help
+usr/share/doc/arb/submit usr/share/arb/lib/submit
Added: trunk/packages/arb/trunk/debian/arb-common.manpages
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.manpages (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.manpages 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+debian/bin/arb_clean.1
Added: trunk/packages/arb/trunk/debian/arb-common.postinst
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.postinst (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.postinst 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,53 @@
+#!/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#
Added: trunk/packages/arb/trunk/debian/arb-common.preinst
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.preinst (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.preinst 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,23 @@
+#!/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#
Added: trunk/packages/arb/trunk/debian/arb-common.templates
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.templates (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.templates 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,6 @@
+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}.
Added: trunk/packages/arb/trunk/debian/arb-doc.doc-base
===================================================================
--- trunk/packages/arb/trunk/debian/arb-doc.doc-base (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-doc.doc-base 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,14 @@
+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: Apps/Science
+
+Format: html
+Index: /usr/share/doc/arb/html/index.html
+Files: /usr/share/doc/arb/html/*
Added: trunk/packages/arb/trunk/debian/arb-doc.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-doc.install (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-doc.install 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,2 @@
+lib/help_html/* usr/share/doc/arb/html
+HELP_SOURCE/oldhelp/arb.ps.gz usr/share/doc/arb/help
Added: trunk/packages/arb/trunk/debian/arb-doc.links
===================================================================
--- trunk/packages/arb/trunk/debian/arb-doc.links (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-doc.links 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+usr/share/doc/arb/html/manual.html usr/share/doc/arb/html/index.html
Added: trunk/packages/arb/trunk/debian/arb.README.debian
===================================================================
--- trunk/packages/arb/trunk/debian/arb.README.debian (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.README.debian 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,106 @@
+Arb for DEBIAN
+--------------
+
+The FTP archive where this version was downloaded from says:
+
++---------------------------------------------------------------------------------+
+| |
+| IMPORTANT - Please read: |
+| |
+| The version in this directory is the latest build from our development team. |
+| Regard this version as 'NOT RELEASED'. |
+| |
+| You are DISALLOWED to supply copies of the files from this directory. |
+| As well you are DISALLOWED to make direct links to the files in this directory. |
+| |
+| Please do not encourage normal ARB users to download version from here. |
+| |
+| This version is completely untested and/or experimental - so it may easily |
+| VAPORIZE all your data, your machine or even yourself. |
+| |
+| |
+| *** Use at your own risk! *** |
+| |
+| |
+| The versions in the subdirectories below this directory are/have been used |
+| by several people at our institute, so they can be regarded as less dangerous |
+| than the latest build. |
+| |
+| Known bugs: |
+| |
+| - Many refresh problems in EDIT4 (2005_03_15 + 2005_03_31) |
+| - Secondary structure editor has problems with base positions |
+| (2005_03_15 + 2005_03_31 + 2005_05_06) |
+| |
++---------------------------------------------------------------------------------+
+
+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.
+ - I applied the arb patches of molphy to the upstream molphy.
+ As the maintainer of the molphy package which is orphaned
+ upstream I included the patches from Arb and thus I expect
+ the Debian packaged version to run with the symlinks from Arb.
+ - 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 overriden by a separat package if
+ necessary.
+ - libmotif: I tried to compile Arb against liblesstif. The
+ package builds fine but when running the program some controls
+ are just missing or not usable. I will try future versions
+ of lesstif and Arb.
+
+
+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 <tille at debian.org>, Sat, 20 Oct 2001 08:09:48 +0200
Added: trunk/packages/arb/trunk/debian/arb.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb.install (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.install 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,7 @@
+bin/[A-Zabcd-z]* usr/lib/arb/bin
+debian/bin/arb usr/bin
+debian/bin/arb-add-pt-server usr/bin
+debian/bin/arb-kill usr/bin
+debian/arb.xpm usr/share/arb
+debian/conf/arb_tcp.dat etc/arb
+debian/conf/arb.conf etc/arb
Added: trunk/packages/arb/trunk/debian/arb.links
===================================================================
--- trunk/packages/arb/trunk/debian/arb.links (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.links 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,39 @@
+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
Added: trunk/packages/arb/trunk/debian/arb.manpages
===================================================================
--- trunk/packages/arb/trunk/debian/arb.manpages (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.manpages 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,3 @@
+debian/bin/arb.1
+debian/bin/arb-kill.1
+debian/bin/arb-add-pt-server.1
Added: trunk/packages/arb/trunk/debian/arb.menu
===================================================================
--- trunk/packages/arb/trunk/debian/arb.menu (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.menu 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,2 @@
+?package(arb):needs="X11" section="Applications/Science/Biology" \
+ title="Arb" icon="/usr/share/arb/arb.xpm" command="/usr/bin/arb"
Added: trunk/packages/arb/trunk/debian/arb.postinst
===================================================================
--- trunk/packages/arb/trunk/debian/arb.postinst (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.postinst 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,26 @@
+#!/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
+ /usr/sbin/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 ${CONFFILE}`
+fi
+
+#DEBHELPER#
Added: trunk/packages/arb/trunk/debian/arb.xpm
===================================================================
--- trunk/packages/arb/trunk/debian/arb.xpm (rev 0)
+++ trunk/packages/arb/trunk/debian/arb.xpm 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,18 @@
+/* XPM */
+static char * arb_xpm[] = {
+"31 13 2 1",
+" c None",
+". c #000000",
+" .. ",
+" ... .. ",
+" .... .. ",
+" ..... .. ",
+" ...... ... ... ",
+" ... .. .... ..... ",
+" ... .. ...... ..... ",
+" ... .. .. ..",
+" ... .. .. ..",
+" ... .. ... ..",
+" ... .. .. ...",
+" ... .. .. ........ ",
+"... .. .. ...... "};
Added: trunk/packages/arb/trunk/debian/bin/arb
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,56 @@
+#!/bin/sh
+CONF=/etc/arb/arb.conf
+USERCONF=${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 <<EOF
+Warning: User $USER is no member of group arb and thus not allowed to write to
+ /var/lib/arb. This might restrict the functionality of arb.
+ Please ask your system administrator to run
+
+ dpkg-reconfigure arb-common
+
+ to incllude user $USER into the group of users which have full
+ privilegs to run arb.
+
+EOF
+fi
+
+export ARBHOME=/usr/lib/arb
+${ARBHOME}/bin/arb
Added: trunk/packages/arb/trunk/debian/bin/arb-add-pt-server
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb-add-pt-server (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb-add-pt-server 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,83 @@
+#!/usr/bin/perl
+# Allow users of group "arb" to add pt_server entries
+# Andreas Tille <tille at debian.org>
+# 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 = $port_max = 0;
+
+while ( <CFG> ) {
+ if ( ! /^[^#]*\bARB_PT_SERVER/ ) {
+ print TMP ;
+ next ;
+ }
+ chomp ;
+ s/\s*#.*// ;
+ if ( /ARB_PT_SERVER([0-9]+)\s+localhost:([0-9]{4})\s+arb_pt_server\s+-D(.+)$/ ) {
+ $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 $PTServerDir does not exist.\n" ;
+ exit -1 ;
+}
+ at ptservers = grep { /^$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");
Added: trunk/packages/arb/trunk/debian/bin/arb-add-pt-server.1
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb-add-pt-server.1 (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb-add-pt-server.1 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,30 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" 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 <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/arb/trunk/debian/bin/arb-kill
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb-kill (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb-kill 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,18 @@
+#!/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/"`
+ rm -f /tmp/arb_pids_${USER}_*
+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/"`
+ rm -f /tmp/arb_pids_*_*
+fi
Added: trunk/packages/arb/trunk/debian/bin/arb-kill.1
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb-kill.1 (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb-kill.1 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,30 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" 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
+.B arb-kill [--all]
+\- 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
+
+.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 <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/arb/trunk/debian/bin/arb.1
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb.1 (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb.1 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,36 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" 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 <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/arb/trunk/debian/bin/arb_clean.1
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb_clean.1 (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb_clean.1 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,28 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" 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 <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/arb/trunk/debian/bin/arb_create_debian_conffile
===================================================================
--- trunk/packages/arb/trunk/debian/bin/arb_create_debian_conffile (rev 0)
+++ trunk/packages/arb/trunk/debian/bin/arb_create_debian_conffile 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,20 @@
+#!/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
Added: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog (rev 0)
+++ trunk/packages/arb/trunk/debian/changelog 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,197 @@
+arb (0.0.20071029-1) unstable; urgency=low
+
+ * New upstream version
+ * Added Build-Depends libglew-dev which is needed for 3D version
+ * Added Build-Depends libxpm4-dev according to the advise of
+ Charles Plessy <charles-debian-nospam at plessy.org> 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
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <elmar at pruesse.net>)
+ Closes: #333391
+ * Updated Swedish debconf template (Thanks to Daniel Nylander
+ <yeager at lidkoping.net>)
+ Closes: #332788
+ * Updated French debconf template (Thanks to Jean-Luc Coulon
+ <jean-luc.coulon at wanadoo.fr>)
+ Closes: #333108
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <yeager at lidkoping.net>
+ 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 <tille at debian.org> 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 <Petr.Salinger at t-systems.cz>)
+ * Reduced number of architectures to the set that features xviewg-dev
+
+ -- Andreas Tille <tille at debian.org> 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 <Petr.Salinger at t-systems.cz>)
+
+ -- Andreas Tille <tille at debian.org> 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 <barbier at debian.org>)
+ Closes: #325062
+ * Depends: freeglut3-dev | libglu-dev
+ * Build-Depends: libpng12-dev (Thanks to Petr Salinger <Petr.Salinger at t-systems.cz>)
+ * Some patches that where necessary for building with gcc 4.0.x
+ (Thanks to Petr Salinger <Petr.Salinger at t-systems.cz>)
+ * arb-common: Depends: adduser
+ * arb-common.config: Removed bashism
+
+ -- Andreas Tille <tille at debian.org> 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 <Igor.Jasa at seznam.cz>
+ Closes: #318442
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Tue, 16 Nov 2004 18:23:59 +0100
+
+arb (0.0.20041112-1) unstable; urgency=low
+
+ * Inoffcial test release.
+
+ -- Andreas Tille <tille at debian.org> Fri, 12 Nov 2004 13:15:16 +0100
+
Added: trunk/packages/arb/trunk/debian/compat
===================================================================
--- trunk/packages/arb/trunk/debian/compat (rev 0)
+++ trunk/packages/arb/trunk/debian/compat 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+5
Added: trunk/packages/arb/trunk/debian/conf/arb.conf
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb.conf (rev 0)
+++ trunk/packages/arb/trunk/debian/conf/arb.conf 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,19 @@
+# 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
Added: trunk/packages/arb/trunk/debian/conf/arb_ntree.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_ntree.dat (rev 0)
+++ trunk/packages/arb/trunk/debian/conf/arb_ntree.dat 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,4 @@
+#*********** 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
Added: trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat (rev 0)
+++ trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,27 @@
+#*********** 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<n> localhost:303<n> arb_pt_server -D<path_to_arb_database>
+# where <n> 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
Added: trunk/packages/arb/trunk/debian/conf/arb_tcp.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_tcp.dat (rev 0)
+++ trunk/packages/arb/trunk/debian/conf/arb_tcp.dat 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,67 @@
+#******************* 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) ******************
+#
+#*********** 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
+#*********** 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<n> localhost:303<n> arb_pt_server -D<path_to_arb_database>
+# where <n> 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
Added: trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat (rev 0)
+++ trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,36 @@
+#******************* 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) ******************
+#
Added: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control (rev 0)
+++ trunk/packages/arb/trunk/debian/control 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,116 @@
+Source: arb
+Section: non-free/science
+Priority: extra
+Maintainer: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 5.0), dpatch (>= 2.0), libmotif-dev, xviewg-dev, rxp, lynx, sablotron, libtiff4-dev, libxaw7-dev, kaffe | free-java-sdk, freeglut3-dev | libglu-dev, libglew-dev, libpng12-dev, x11proto-print-dev, libxpm-dev, libxp-dev, libglw1-mesa-dev
+Standards-Version: 3.7.2
+
+Package: arb
+Architecture: alpha arm hppa i386 m68k mips mipsel powerpc s390 sparc
+Depends: ${shlibs:Depends}, libarb (= ${binary:Version}), arb-common (= ${source:Version}), phylip (>= 3.6b), fastdnaml (>= 1.2.2-4), readseq (>= 1-1), tree-puzzle (>=5.0-3), molphy, ssh, transfig
+Recommends: xfig
+Suggests: arb-database, gnuplot, gv
+Description: [Biology] Integrated package for data handling and analysis
+ Important: This version is the latest build from the ARB development team.
+ Regard this version as 'NOT RELEASED'.
+ .
+ Please do not encourage normal ARB users to use this software. It is intended
+ for previews and to support the ARB development.
+ .
+ This version is completely untested and/or experimental - so it may easily
+ VAPORIZE all your data, your machine or even yourself. Use at your own risk!
+ .
+ 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.
+ .
+ Architecture dependend binaries of Arb.
+ .
+ Home: http://www.arb-home.de/
+
+Package: libarb
+Architecture: alpha arm hppa i386 m68k mips mipsel powerpc s390 sparc
+Depends: ${shlibs:Depends}
+Recommends: arb
+Description: [Biology] Integrated package for data handling and analysis
+ Important: This version is the latest build from the ARB development team.
+ Regard this version as 'NOT RELEASED'.
+ .
+ Please do not encourage normal ARB users to use this software. It is intended
+ for previews and to support the ARB development.
+ .
+ This version is completely untested and/or experimental - so it may easily
+ VAPORIZE all your data, your machine or even yourself. Use at your own risk!
+ .
+ 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.
+ .
+ Home: http://www.arb-home.de/
+
+Package: arb-common
+Architecture: all
+Depends: arb-doc (= ${source:Version}), adduser, gs | postscript-preview, gv | postscript-viewer, perl-modules, ${perl:Depends}, ${misc:Depends}
+Recommends: arb
+Suggests: xview-clients
+Description: [Biology] Integrated package for data handling and analysis
+ Important: This version is the latest build from the ARB development team.
+ Regard this version as 'NOT RELEASED'.
+ .
+ Please do not encourage normal ARB users to use this software. It is intended
+ for previews and to support the ARB development.
+ .
+ This version is completely untested and/or experimental - so it may easily
+ VAPORIZE all your data, your machine or even yourself. Use at your own risk!
+ .
+ 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.
+ .
+ Architecture independend scripts of Arb.
+ .
+ Home: http://www.arb-home.de/
+
+Package: arb-doc
+Architecture: all
+Depends: gs | postscript-preview, gv | postscript-viewer
+Suggests: arb
+Description: [Biology] Integrated package for data handling and analysis
+ Important: This version is the latest build from the ARB development team.
+ Regard this version as 'NOT RELEASED'.
+ .
+ Please do not encourage normal ARB users to use this software. It is intended
+ for previews and to support the ARB development.
+ .
+ This version is completely untested and/or experimental - so it may easily
+ VAPORIZE all your data, your machine or even yourself. Use at your own risk!
+ .
+ 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.
+ .
+ Documentation.
+ .
+ Home: http://www.arb-home.de/
Added: trunk/packages/arb/trunk/debian/copyright
===================================================================
--- trunk/packages/arb/trunk/debian/copyright (rev 0)
+++ trunk/packages/arb/trunk/debian/copyright 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,341 @@
+This package was debianized by Andreas Tille tille at debian.org on
+Thu, 3 Jun 2004 11:17:55 +0200.
+
+It was downloaded from
+
+ http://www2.mikro.biologie.tu-muenchen.de/download/ARB/pre_release/
+
+The FTP archive where this version was downloaded from says:
+
++---------------------------------------------------------------------------------+
+| |
+| IMPORTANT - Please read: |
+| |
+| The version in this directory is the latest build from our development team. |
+| Regard this version as 'NOT RELEASED'. |
+| |
+| You are DISALLOWED to supply copies of the files from this directory. |
+| As well you are DISALLOWED to make direct links to the files in this directory. |
+| |
+| Please do not encourage normal ARB users to download version from here. |
+| |
+| This version is completely untested and/or experimental - so it may easily |
+| VAPORIZE all your data, your machine or even yourself. |
+| |
+| |
+| *** Use at your own risk! *** |
+| |
+| |
+| The versions in the subdirectories below this directory are/have been used |
+| by several people at our institute, so they can be regarded as less dangerous |
+| than the latest build. |
+| |
+| Known bugs: |
+| |
+| - Many refresh problems in EDIT4 (2005_03_15 + 2005_03_31) |
+| - Secondary structure editor has problems with base positions |
+| (2005_03_15 + 2005_03_31 + 2005_05_06) |
+| |
++---------------------------------------------------------------------------------+
+
+Ralf Westram, who is one of the authors below, wrote in private mail:
+
+> ------------------------------
+>
+> Hereby Andreas Tille is granted the right to build debian-pakets of
+> the ARB software http://www.arb-home.de/ and publish them on debian
+> mirrors.
+>
+> 1.9.2005
+> Ralf Westram <westram at arb-home.de>
+>
+> ------------------------------
+
+
+The authors are
+ Department of Microbiology:
+
+ Dr. Wolfgang Ludwig (Biologist) <ludwig at arb-home.de>
+ Task: Group Leader; Inventor of ARB, knows everything about it
+
+ Ralf Westram (Computer scientist) <westram at reallysoft.de>
+ Task: General ARB development
+
+ Dr. Lothar Richter (Biologist) <richter at arb-home.de>
+ Task: ARB Database Curation and Automatization
+
+ Arno Buchner (Biologist) <buchner at arb-home.de>
+ Task: ARB Database Curation and Genomics
+
+ Department of Computer Science:
+
+ Prof. Dr. Thomas Ludwig (Computer Scientist) <thomas.ludwig at informatik.uni-heidelberg.de>
+ Task: Computer Science Supervisor
+
+ Dr. Harald Meier (Biologist) <meierh at arb-home.de>
+ Task: ARB GENOME programming
+
+ Gangolf Jobb (Biologist) <jobb at arb-home.de>
+ Task: Development and integration of alignment- and tree-generation-software
+
+The homepage is
+ http://www.arb-home.de/
+
+
+Copyrights:
+
+ARB copyright and license information
+
+ * 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.
+
+
+Copyright notices for programs distributes together with ARB
+
+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.
+
+
+PHYLIP
+
+(c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington.
+Permission is granted to copy this document provided that no fee is charged for
+it and that this copyright notice is not removed.
+
+ [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.
+
+LSADT
+
+ * LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO PROXIMITY DATA
+ * GEERT DE SOETE -- VERSION 1.01 - FEB. 1983
+ VERSION 1.02 - JUNE 1983
+ VERSION 1.03 - JULY 1983
+
+ * C version by Michael Macuikenas, University of Illinois
+ * REFERENCE: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
+ ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48, 621-626.
+ DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
+ DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18, 387-393.
+
+
+ * REMARKS *
+ -----------
+
+ 1) THE PROGRAM USES SUBROUTINES FROM THE PORT LIBRARY FOR
+ ERROR HANDLING, DYNAMIC STORAGE ALLOCATION AND SPECIFICATION
+ OF MACHINE-DEPENDENT CONSTANTS.
+ CF. FOX, P.A., HALL, A.D., & SCHRYER, N.L.
+
+ THE PORT MATHEMATICAL SUBROUTINE LIBRAY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 104-126.
+ ALGORITHM 528. FRAMEWORK FOR A PORTABLE LIBRARY. ACM TRANS. ON MATH. SOFTW., 1978, 4, 177-188.
+
+ 2) UNIFORMLY DISTRIBUTED RANDOM NUMBERS ARE GENERATED BY A PROCEDURE DUE
+ TO SCHRAGE. CF. SCHRAGE, L. A MORE PORTABLE FORTRAN RANDOM NUMBER GENERATOR.
+ ACM TRANS. ON MATH. SOFTW., 1979, 5, 132-138.
+
+ 3) SUBROUTINES VA14AD AND VA14AC ARE ADAPTED FROM THE HARWELL SUBROUTINE
+ LIBRARY (1979 EDITION).
+
+ 4) ALTHOUGH THIS PROGRAM HAS BEEN CAREFULLY TESTED, THE AUTHOR DISCLAIMS
+ ANY RESPONSABILITY FOR POSSIBLE ERRORS.
+
+ [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.
+
+
+BLAST
+
+/* ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ * National Center for Biotechnology Information
+ *
+ * This software/database is a "United States Government Work" under the
+ * terms of the United States Copyright Act. It was written as part of
+ * the authors official duties as a United States Government employee and
+ * thus cannot be copyrighted. This software/database is freely available
+ * to the public for use. The National Library of Medicine and the U.S.
+ * Government have not placed any restriction on its use or reproduction.
+ *
+ * Although all reasonable efforts have been taken to ensure the accuracy
+ * and reliability of the software and data, the NLM and the U.S.
+ * Government do not and cannot warrant the performance or results that
+ * may be obtained by using this software or data. The NLM and the U.S.
+ * Government disclaim all warranties, express or implied, including
+ * warranties of performance, merchantability or fitness for any particular
+ * purpose.
+ *
+ * Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================*/
+Warren Gish
+NCBI/NLM
+
+ [Remark from the Debian package maintainer Andreas Tille]
+ This is not used in the binary package because it is available as
+ official Debian package named blast2 which is builded from the
+ ncbi-tools6 source package and has a free license (see this package).
+
+CONVERT_ALN
+
+ 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.
+
+
+TREETOOL
+
+ * Written by Mike Maciukenas, at the RDP, with design and implementation guidance by Gary Olsen, Niels Larsen, Carl Woese.
+ * Copyright (c) 1991, University of Illinois board of trustess. All rights reserved.
+ * Treetool is a copyrighted program, not in the public domain. It is provided free of charge, and permission is granted to copy and dirstribute, provided that it is not done for profit, and that all copyright messages remain present and intact.
+
+ [Remark from the Debian package maintainer Andreas Tille]
+ This is not used in the binary package because the Debian
+ package is used which is in the non-free part of Debian.
+ Remark: It was not possible to contact the original author who
+ stated that it would be planned to release the program under GPL
+ but applied no license at all to the source package.
+
+fastdnaml
+
+ * fastDNAml, a program for estimation of phylogenetic trees from sequences.
+ Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
+ * This program is free software; you may redistribute it and/or modify it under
+ the terms of the GNU General Public License as published by the Free Software
+ Foundation; either version 2 of the License, or (at your option) any later
+ version.
+
+ On Debian GNU/Linux systems you can find the text of this license under
+ /usr/share/common-licenses/GPL
+
+ * This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ * For any other enquiries write to Gary J. Olsen, Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
+ * Or send E-mail to gary at phylo.life.uiuc.edu
+ * fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
+ * Copyright notice from dnaml:
+
+ version 3.3. (c) Copyright 1986, 1990 by the University of Washington and Joseph Felsenstein. Written by Joseph Felsenstein. 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.
+ * When publishing work that based on results from fastDNAml please cite:
+ o Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
+ o and
+ o Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.
+
+ [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).
+
+
+RAxML
+ A slightly older version than the code contained in arb/GDE/RAxML can
+ be obtained from
+ http://www.lrr.in.tum.de/~stamatak/index_old.html
+ A much newer version than in the arb source is at.
+ http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
+ Neither version comes with a copyright statement but in
+ arb/GDE/RAxML/softwaredisclaimer you can read:
+
+ LEGAL DISCLAIMER
+
+ THIS SOFTWARE IS PROVIDED BY ALEXANDROS STAMATAKIS AND THE INSTITUTE OF
+ COMPUTER SCIENCE, FOUNDATION FOR RESEARCH AND TECHNOLOGH HELLAS
+ 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 AUTHOR 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. NO COMMERCIAL USE OR COMMERCIAL
+ REDISTRIBUTION OF THIS SOFTWARE IS AUTHORIZED. ANY PUBLICATION
+ BASED ON THE USE OF THIS SOFTWARE MUST EXPLICITLY ACKNOWLEDGE ITS
+ USE AND SHOULD CITE THE APPROPRIATE PAPER(S) LISTED IN THE README
+ FILE.
+
+
+[Additions from the Debian package maintainer Andreas Tille]
+The source package also contains the external software packages
+
+ treepuzzle:
+ This is not used in the binary package because it is available as
+ official Debian package and has a free license (see this package).
+
+ readseq:
+ This is not used in the binary package because it is available as
+ official Debian package and has a free license (see this package).
+
+ molphy:
+ This is also not used in the binary package because the Debian
+ package is used which is in the non-free part of Debian.
+ Remark: The e-mail address of the author of this program was
+ recently found and chances are not bad that the open license
+ issues can be solved for this package.
+
Added: trunk/packages/arb/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/arb/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/arb/trunk/debian/get-orig-source 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,45 @@
+#!/bin/sh -e
+NAME=arb
+UTARBALL=${NAME}src.tgz
+downloadurl=http://www2.mikro.biologie.tu-muenchen.de/download/ARB/latest_build/
+
+RemoveFilesFromSource="GDEHELP/HELP_DOC_GEN/* GDEHELP/HELP_GEN/* GDEHELP/ARB_GDEmenus GDEHELP/helpfiles.lst HELP_SOURCE/_index.html NTREE/nt_date.h lib/ARB.pm"
+
+if [ -e ${UTARBALL} ] ; then
+ echo "Using existing tarball ${UTARBALL}"
+else
+ wget --quiet ${downloadurl}/${UTARBALL}
+fi
+
+rm -rf tmp
+mkdir -p tmp/arbdir
+cd tmp/arbdir
+tar -xzf ../../"$UTARBALL"
+
+VERSION=`ls -lt | grep '^[^d]rw.r' | sed -e '2,$d' -e 's/^.[-rwxr]\{9\} \+[0-9] \w\+ \w\+[[:space:]]\+[0-9]\+ \([0-9]\{4\}\)-\([0-9]\{2\}\)-\([0-9]\{2\}\).*/0.0.\1\2\3/'`
+
+cd ..
+mv arbdir "$NAME"-"$VERSION"
+cd "$NAME"-"$VERSION"
+
+rm -rf `find . -type d -name CVS`
+rm -rf `find . -type f -name ".#*"`
+rm -rf ${RemoveFilesFromSource}
+find . -name .cvsignore -exec rm -f \{\} \;
+rm -f HELP_SOURCE/oldhelp/help.tar
+find lib ! -newer lib/config.HP-UX -exec touch -r lib/config.HP-UX \{\} \;
+find SH ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \;
+find PERL_SCRIPTS ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \;
+find HELP_SOURCE ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \;
+rm -f SH/arb_oneach
+
+
+chmod 644 lib/submit/*
+
+cd ..
+
+GZIP=-9 tar -czf "$NAME"_"$VERSION".orig.tar.gz "$NAME"-"$VERSION"
+
+mv "$NAME"_"$VERSION".orig.tar.gz ..
+cd ..
+rm -rf tmp
Added: trunk/packages/arb/trunk/debian/libarb.install
===================================================================
--- trunk/packages/arb/trunk/debian/libarb.install (rev 0)
+++ trunk/packages/arb/trunk/debian/libarb.install 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+lib/*.so usr/lib/
Added: trunk/packages/arb/trunk/debian/lintian.overrides
===================================================================
--- trunk/packages/arb/trunk/debian/lintian.overrides (rev 0)
+++ trunk/packages/arb/trunk/debian/lintian.overrides 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,3 @@
+# 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/share/arb/lib/macro.head
Added: trunk/packages/arb/trunk/debian/patches/00list
===================================================================
--- trunk/packages/arb/trunk/debian/patches/00list (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/00list 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,4 @@
+20_config.makefiles.dpatch
+20_developer_tools.dpatch
+20_Makefiles.dpatch
+20_perl_scripts.dpatch
Added: trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,89 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_Makefiles.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fixing several Makefiles
+
+ at DPATCH@
+
+diff -urbN arb-0.0.20071029.orig/ARBDB2/Makefile arb-0.0.20071029/ARBDB2/Makefile
+--- arb-0.0.20071029.orig/ARBDB2/Makefile 2007-10-29 14:53:19.000000000 +0100
++++ arb-0.0.20071029/ARBDB2/Makefile 2007-11-05 11:54:29.000000000 +0100
+@@ -1,7 +1,12 @@
+ # 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)
+
+diff -urbN arb-0.0.20071029.orig/ARBDBS/Makefile arb-0.0.20071029/ARBDBS/Makefile
+--- arb-0.0.20071029.orig/ARBDBS/Makefile 2007-10-29 14:53:19.000000000 +0100
++++ arb-0.0.20071029/ARBDBS/Makefile 2007-11-05 11:55:13.000000000 +0100
+@@ -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) $(GB_X)
+diff -urbN arb-0.0.20071029.orig/Makefile arb-0.0.20071029/Makefile
+--- arb-0.0.20071029.orig/Makefile 2007-10-29 14:53:19.000000000 +0100
++++ arb-0.0.20071029/Makefile 2007-11-05 12:00:29.000000000 +0100
+@@ -108,7 +108,7 @@
+
+ ALLOWED_GCC_295_VERSIONS=2.95.3
+ ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3
+-ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1
++ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3
+ ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
+
+ GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)
+diff -urbN arb-0.0.20071029.orig/NAMES_COM/Makefile arb-0.0.20071029/NAMES_COM/Makefile
+--- arb-0.0.20071029.orig/NAMES_COM/Makefile 2007-06-29 21:04:04.000000000 +0200
++++ arb-0.0.20071029/NAMES_COM/Makefile 2007-09-12 15:59:27.000000000 +0200
+@@ -27,7 +27,7 @@
+ # $(MAKE) -r -f AISC/Makefile depends
+
+ clean:
+- $(MAKE) $(makeflags) -f AISC/Makefile clean
++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean
+
+ # DO NOT DELETE
+
+diff -urbN arb-0.0.20071029.orig/ORS_COM/Makefile arb-0.0.20071029/ORS_COM/Makefile
+--- arb-0.0.20071029.orig/ORS_COM/Makefile 2007-06-29 21:04:05.000000000 +0200
++++ arb-0.0.20071029/ORS_COM/Makefile 2007-09-12 16:00:49.000000000 +0200
+@@ -28,7 +28,7 @@
+ # @echo "no automatic dependencies for ORS_COM - skipped"
+
+ clean:
+- $(MAKE) $(makeflags) -f AISC/Makefile clean
++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean
+
+ # DO NOT DELETE
+
+diff -urbN arb-0.0.20071029.orig/PROBE_COM/Makefile arb-0.0.20071029/PROBE_COM/Makefile
+--- arb-0.0.20071029.orig/PROBE_COM/Makefile 2007-06-29 21:04:05.000000000 +0200
++++ arb-0.0.20071029/PROBE_COM/Makefile 2007-09-12 16:01:29.000000000 +0200
+@@ -30,7 +30,7 @@
+ # @echo "no automatic dependencies for PROBE_COM - skipped"
+
+ clean:
+- $(MAKE) $(makeflags) -f AISC/Makefile clean
++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean
+
+ # DO NOT DELETE
+
Added: trunk/packages/arb/trunk/debian/patches/20_config.makefiles.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_config.makefiles.dpatch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/20_config.makefiles.dpatch 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,69 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_config.makefiles.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Create config.makefiles for building on a Debian machine
+
+ at DPATCH@
+
+diff -urbN arb-0.0.20071029.orig/config.makefile arb-0.0.20071029/config.makefile
+--- arb-0.0.20071029.orig/config.makefile 1970-01-01 01:00:00.000000000 +0100
++++ arb-0.0.20071029/config.makefile 2007-09-08 18:16:18.000000000 +0200
+@@ -0,0 +1,57 @@
++# --------------------------------------------------------------------------------
++# 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)
++
++# --------------------------------------------------------------------------------
++# 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
++
++# uncomment next line for REDHAT systems
++# REDHAT = 1
++
++# ********* Mac OSX ********
++
++# MACH = DARWIN#
++# DARWIN = 1
++
++# ********* SUN4 / acc CC / dynamic ********
++
++# MACH = SUN4#
++# SUN4 = 1# # Exportable Version
++
++# MACH = SUN5#
++# SUN5 = 1
++# ECGS = 1# use GCC?
++# SUN_WS_50 = 1 # compile with Workshop 5.0
++
++# ********* HP ****************
++# HPCC = 1
++# HPGCC = 1
++# MACH = HP#
++
++# ******* SGI ***********
++# SGI = 1
++# MACH = SGI#
++
++# ******* DIGITAL OSF ***********
++# DIGITAL = 1
++# MACH = DIGITAL#
++
Added: trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,23 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_developer_tools.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: This tool seems to be only interesting for developers of Arb. Because
+## DP: this fact is not documented it is installed with the package but needs
+## DP: fixing.
+
+ at DPATCH@
+
+diff -urbN arb-0.0.20071029.orig/util/arb_export arb-0.0.20071029/util/arb_export
+--- arb-0.0.20071029.orig/util/arb_export 2003-08-22 23:07:55.000000000 +0200
++++ arb-0.0.20071029/util/arb_export 2005-10-07 08:19:30.000000000 +0200
+@@ -28,6 +28,6 @@
+ # export names.dat:
+ echo "****************************************"
+ echo "exporting names.dat"
+-echo gzip </usr/arb/lib/nas/names.dat >$dest/xtra/names.dat.gz
+-gzip </usr/arb/lib/nas/names.dat >$dest/xtra/names.dat.gz
+-
++ARBHOME=${ARBHOME:-"/usr/arb/lib"}
++echo gzip <${ARBHOME}/nas/names.dat >$dest/xtra/names.dat.gz
++gzip <${ARBHOME}/nas/names.dat >$dest/xtra/names.dat.gz
Added: trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,17 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_perl_scripts.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fix path to perl
+
+ at DPATCH@
+
+diff -urbN arb-0.0.20071029.orig/PERL_SCRIPTS/IFTHELP/embl_gen_long_features.pl arb-0.0.20071029/PERL_SCRIPTS/IFTHELP/embl_gen_long_features.pl
+--- arb-0.0.20071029.orig/PERL_SCRIPTS/IFTHELP/embl_gen_long_features.pl 2005-03-18 15:28:12.000000000 +0100
++++ arb-0.0.20071029/PERL_SCRIPTS/IFTHELP/embl_gen_long_features.pl 2005-05-31 07:29:25.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!perl
++#!/usr/bin/perl
+ # =============================================================== #
+ # #
+ # File : embl_gen_long_features.pl #
Added: trunk/packages/arb/trunk/debian/po/POTFILES.in
===================================================================
--- trunk/packages/arb/trunk/debian/po/POTFILES.in (rev 0)
+++ trunk/packages/arb/trunk/debian/po/POTFILES.in 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1 @@
+[type: gettext/rfc822deb] arb-common.templates
Added: trunk/packages/arb/trunk/debian/po/cs.po
===================================================================
--- trunk/packages/arb/trunk/debian/po/cs.po (rev 0)
+++ trunk/packages/arb/trunk/debian/po/cs.po 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,48 @@
+#
+# 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: tille at debian.org\n"
+"POT-Creation-Date: 2005-10-07 07:35+0200\n"
+"PO-Revision-Date: 2005-07-13 19:16+0200\n"
+"Last-Translator: Igor Jasa <Igor.Jasa at seznam.cz>\n"
+"Language-Team: Czech <debian-110n-czech at lists.debian.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=ISO-8859-2\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid "Arb users:"
+msgstr ""
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid ""
+"Please choose, among the list of all unprivileged users of the system, those "
+"who will be allowed running ${pkg}."
+msgstr ""
+
+#~ msgid ""
+#~ "Here is a list of all normal users of the system. Now you can select "
+#~ "those users who should be able to use ARB."
+#~ msgstr ""
+#~ "Tady je seznam v¹ech bì¾ných u¾ivatelù systému. Teï mù¾ete vybrat ty "
+#~ "u¾ivatele, kteøí by mìli být mo¾nost pou¾ívat ARB."
+
+#~ msgid "Please specify the Arb users!"
+#~ msgstr "Prosím specifikujte u¾ivatele Arb!"
Added: trunk/packages/arb/trunk/debian/po/de.po
===================================================================
--- trunk/packages/arb/trunk/debian/po/de.po (rev 0)
+++ trunk/packages/arb/trunk/debian/po/de.po 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,41 @@
+#
+# 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: tille at debian.org\n"
+"POT-Creation-Date: 2005-10-07 07:35+0200\n"
+"PO-Revision-Date: 2005-10-07 08:18+0100\n"
+"Last-Translator: Andreas Tille <tille at debian.org>\n"
+"Language-Team: German <debian-l10n-german at lists.debian.org>\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:4
+msgid "Arb users:"
+msgstr "Arb Nutzer:"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid ""
+"Please choose, among the list of all unprivileged users of the system, those "
+"who will be allowed running ${pkg}."
+msgstr ""
+"Bitte wählen Sie aus der Liste aller nichtprivilegierten Nutzer des Systems "
+"all diejenigen aus, die ${pkg} nutzen dürfen."
Added: trunk/packages/arb/trunk/debian/po/fr.po
===================================================================
--- trunk/packages/arb/trunk/debian/po/fr.po (rev 0)
+++ trunk/packages/arb/trunk/debian/po/fr.po 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,38 @@
+# 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: tille at debian.org\n"
+"POT-Creation-Date: 2005-10-07 07:35+0200\n"
+"PO-Revision-Date: 2005-10-08 22:31+0200\n"
+"Last-Translator: Jean-Luc Coulon (f5ibh) <jean-luc.coulon at wanadoo.fr>\n"
+"Language-Team: French <debian-l10n-french at lists.debian.org>\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:4
+msgid "Arb users:"
+msgstr "Liste des utilisateurs d'Arb :"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+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 privilégiés du système, "
+"ceux qui seront autorisés à utiliser ${pkg}."
Added: trunk/packages/arb/trunk/debian/po/sv.po
===================================================================
--- trunk/packages/arb/trunk/debian/po/sv.po (rev 0)
+++ trunk/packages/arb/trunk/debian/po/sv.po 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,38 @@
+# 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: tille at debian.org\n"
+"POT-Creation-Date: 2005-10-07 07:35+0200\n"
+"PO-Revision-Date: 2005-10-09 18:16+0200\n"
+"Last-Translator: Daniel Nylander <po at danielnylander.se>\n"
+"Language-Team: Swedish <sv at li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=iso-8859-1\n"
+"Content-Transfer-Encoding: 8bit"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid "Arb users:"
+msgstr "Arb användare:"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid ""
+"Please choose, among the list of all unprivileged users of the system, those "
+"who will be allowed running ${pkg}."
+msgstr ""
+"Välj i listan av opriviligerade användare på systemet, de som ska tillåtas att köra ${pkg}."
Added: trunk/packages/arb/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/arb/trunk/debian/po/templates.pot (rev 0)
+++ trunk/packages/arb/trunk/debian/po/templates.pot 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,31 @@
+# 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 <EMAIL at ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"Report-Msgid-Bugs-To: tille at debian.org\n"
+"POT-Creation-Date: 2005-10-07 07:35+0200\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
+"Language-Team: LANGUAGE <LL at li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=CHARSET\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid "Arb users:"
+msgstr ""
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:4
+msgid ""
+"Please choose, among the list of all unprivileged users of the system, those "
+"who will be allowed running ${pkg}."
+msgstr ""
Added: trunk/packages/arb/trunk/debian/rules
===================================================================
--- trunk/packages/arb/trunk/debian/rules (rev 0)
+++ trunk/packages/arb/trunk/debian/rules 2007-11-05 19:22:14 UTC (rev 759)
@@ -0,0 +1,233 @@
+#!/usr/bin/make -f
+# debian/rules for arp using dpatch
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# only necessary for the get-orig-source target
+# version=2005_05_26
+version=20071029
+# downloadurl=http://www2.mikro.biologie.tu-muenchen.de/download/ARB/pre_release/
+# downloadurl=http://www2.mikro.biologie.tu-muenchen.de/download/ARB/pre_release/$(version)/
+downloadurl=http://www2.mikro.biologie.tu-muenchen.de/download/ARB/latest_build/
+
+pkg=arb
+pkgcom=$(pkg)-common
+pkgdoc=$(pkg)-doc
+### pkgnas=$(pkg)-nas
+### do not build server-package any more
+### pkgserv=$(pkg)-server
+common=debian/$(pkgcom)
+
+build: build-stamp debian/po/templates.pot
+build-stamp: patch
+ dh_testdir
+
+ mkdir -p LIBLINK
+ mkdir -p MAKEBIN
+ mkdir -p lib/help
+ export ARBHOME=`pwd` ; \
+ export LC_ALL=C ; \
+ export PATH=$${ARBHOME}/bin:$${PATH} ; \
+ export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \
+ $(MAKE) all
+ export ARBHOME=`pwd` ; \
+ export LC_ALL=C ; \
+ export PATH=$${ARBHOME}/bin:$${PATH} ; \
+ export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \
+ $(MAKE) arbxtras
+
+ touch build-stamp
+
+# 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
+
+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
+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
+
+clean: clean1 unpatch
+clean1:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Make does only work if config.makefile exists which is only the
+ # case when dpatch has installed the patches. So there is neither
+ # a need nor the expection of success if config.makefile is missing
+ if [ -f config.makefile ] ; then $(MAKE) clean ; fi
+ # fix broken clean process
+ find . -type f -name "*.a" -exec rm -f \{\} \;
+ find . -type f -name "*.o" -exec rm -f \{\} \;
+ find . -type f -name "*.so" -exec rm -f \{\} \;
+ 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)
+
+ dh_clean
+
+install:
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ dh_install
+ dh_link
+
+ # 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/arb/\2/\1?' debian/arb-nas.install | grep debian/arb` ; do \
+ rm -f $${arbfile} ; \
+ done ; \
+ fi
+
+ # Install lintian.overrides
+ cp -a debian/lintian.overrides debian/arb-common/usr/share/lintian/overrides/arb-common
+
+ # Fix permissions
+ chmod 755 debian/arb-common/usr/share/arb/SH/*
+ chmod 644 debian/arb-common/usr/share/arb/lib/pixmaps/*.xpm
+ # Remove thumbnail dir
+ rm -rf debian/arb-common/usr/share/arb/lib/pixmaps/.xvpics
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir -i
+ dh_testroot -i
+ dh_installdebconf -i
+ dh_installdocs -i
+ dh_installexamples -i
+ dh_installmenu -i
+# dh_installlogrotate -i
+# dh_installpam -i
+# dh_installmime -i
+# dh_installinit -i
+ dh_installcron -i
+ dh_installman -i
+ dh_installinfo -i
+ dh_installchangelogs -i
+ dh_link -i
+ dh_compress -i
+ dh_fixperms -i
+ dh_installdeb -i
+ dh_perl -i
+ dh_gencontrol -i
+ dh_md5sums -i
+ dh_builddeb -i
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir -a
+ dh_testroot -a
+ dh_installdebconf -a
+ dh_installdocs -a
+ dh_installexamples -a
+ dh_installmenu -a
+# dh_installlogrotate -a
+# dh_installpam -a
+# dh_installmime -a
+# dh_installinit -a
+ dh_installcron -a
+ dh_installman -a
+ dh_installinfo -a
+ dh_installchangelogs -a
+ dh_strip -a
+ dh_link -a
+ dh_compress -a
+ dh_fixperms -a
+ dh_makeshlibs -a
+ dh_installdeb -a
+# dh_perl -a
+ dh_shlibdeps -a -l debian/libarb/usr/lib
+ dh_gencontrol -a
+ dh_md5sums -a
+ dh_builddeb -a
+
+RemoveFilesFromSource=GDEHELP/HELP_DOC_GEN/* GDEHELP/HELP_GEN/* GDEHELP/ARB_GDEmenus GDEHELP/helpfiles.lst \
+ HELP_SOURCE/_index.html NTREE/nt_date.h \
+ lib/ARB.pm \
+ $(RemoveFromSourceAndBuild)
+
+# To update po files as recommended in po-debconf(7)
+debian/po/templates.pot: debian/arb-common.templates
+ @debconf-updatepo
+
+get-orig-source:
+ sh debian/get-orig-source
+
+get-orig-source_old:
+ if [ _"$(version)" = _"" ] ; then \
+ VER=0.0.`date +%Y%m%d` ; \
+ srctgz=$(downloadurl)/$(pkg)src.tgz ; \
+ else \
+ VER=0.0.`echo $(version) | sed 's/_//g'` ; \
+ srctgz=$(downloadurl)/$(pkg)src.tgz ; \
+ fi ; \
+ basetgz=`basename $${srctgz}` ; \
+ if [ ! -e $${basetgz} ] ; then \
+ wget -N $${srctgz} ; \
+ else \
+ if [ "$${basetgz}" -nt "get" ] ; then \
+ echo "Archive $${basetgz} seems to be new. No wget necessary." ; \
+ else \
+ wget -N $${srctgz} ; \
+ fi ; \
+ fi ; \
+ TGZ=`ls $(pkg)src*.tgz | sort | tail -n1` ; \
+ TAR=$(pkg)_$${VER}.orig.tar.gz ; \
+ DIR=$(pkg)-$${VER} ; \
+ if [ -d $${DIR} ] ; then \
+ rm -f $${DIR} ; \
+ fi ; \
+ if [ -f $${DIR} ] ; then \
+ echo "Please remove $${DIR}." ; \
+ exit ; \
+ fi ; \
+ mkdir $${DIR} ; \
+ cd $${DIR} ; \
+ tar -xzf ../$${TGZ} ; \
+ rm -rf `find . -type d -name CVS` ; \
+ rm -rf `find . -type f -name ".#*"` ; \
+ rm -rf $(RemoveFilesFromSource) ; \
+ find . -name .cvsignore -exec rm -f \{\} \; ; \
+ rm -f HELP_SOURCE/oldhelp/help.tar ; \
+ find lib ! -newer lib/config.HP-UX -exec touch -r lib/config.HP-UX \{\} \; ; \
+ find SH ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; ; \
+ find PERL_SCRIPTS ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; ; \
+ find HELP_SOURCE ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; ; \
+ rm -f SH/arb_oneach ; \
+ chmod 644 lib/submit/* ; \
+ cd .. ; \
+ GZIP=-9 tar -czf $${TAR} $${DIR} ; \
+ rm -rf $${DIR}
+
+patch: patch-stamp
+patch-stamp:
+ dpatch apply-all
+ dpatch cat-all >patch-stamp
+ touch patch-stamp
+
+unpatch:
+ dpatch deapply-all
+ rm -rf patch-stamp debian/patched
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/arb/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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