UNIT_TESTER/log_result.pl

+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $reg_summary     = qr/^UnitTester:.*\stests=([0-9]+)\s/;
+my $reg_interrupted = qr/interrupting.*deadlocked.*test/i;
+
+sub log_summary($) {
+  my ($log) = @_;
+  my $interrupted = 0;
+
+  open(LOG,$log) || die "Failed to read '$log' (Reason: $!)";
+  my $line;
+ LINE:  while (defined ($line=<LOG>)) {
+    if ($line =~ $reg_summary) {
+      my $testCount = $1;
+      if ($testCount==0) {
+        ; # looks like all tests in this module have been skipped
+      }
+      else {
+        chomp($line);
+        $line =~ s/^UnitTester:\s*//;
+        my @items = split /\s+/, $line;
+        my $module = undef;
+        my $passed = undef;
+        foreach (@items) {
+          my ($key,$value) = split /=/, $_;
+          if ($key eq 'target') {
+            $value =~ s/\.a//;
+            $module = $value;
+          }
+          elsif ($key eq 'passed') {
+            $passed = $value;
+            if ($passed eq 'ALL') { $passed = $testCount; }
+          }
+        }
+        print "- $module ($passed/$testCount)\n";
+      }
+
+      close(LOG);
+      return;
+    }
+    elsif ($line =~ $reg_interrupted) {
+      $interrupted = 1;
+      last LINE;
+    }
+  }
+
+  close(LOG);
+
+  # no summary found -> problem
+  my $module   = $log; # fallback
+  my $extraMsg = '; invalid logname';
+
+  if ($log =~ /logs\//o) {
+    my $name = $';
+    if ($name =~ /^([^\.]+)\.test/o) {
+      $module = $1;
+      $extraMsg = '';
+    }
+    else {
+      $module = $name;
+    }
+  }
+
+  my $msg = 'no summary; crashed?';
+  if ($interrupted==1) { $msg = 'interrupted; deadlock?'; }
+
+  print "- $module ($msg$extraMsg)\n";
+}
+
+sub main() {
+  my $args = scalar(@ARGV);
+  if ($args!=1) {
+    die "Usage: log_result.pl unittest.log";
+  }
+  else {
+    log_summary($ARGV[0]);
+  }
+}
+main();

debian/copyright

@@ -11,7 +11,9 @@ Files-Excluded: arbsrc*/AISC_COM/Makefile
                 arbsrc*/CON*
                 arbsrc*/D*
                 arbsrc*/E*
-                arbsrc*/G*
+                arbsrc*/GD*
+                arbsrc*/GE*
+                arbsrc*/GL*
                 arbsrc*/HEADERLIBS
                 arbsrc*/HELP_SOURCE
                 arbsrc*/I*
@@ -123,7 +125,25 @@ Files-Excluded: arbsrc*/AISC_COM/Makefile
                 arbsrc*/doc
                 arbsrc*/demo.arb
                 arbsrc*/etc
-                arbsrc*/l*
+                arbsrc*/lib/BUGS
+                arbsrc*/lib/addlibs
+                arbsrc*/lib/arb_default
+                arbsrc*/lib/desktop
+                arbsrc*/lib/dtd
+                arbsrc*/lib/export
+                arbsrc*/lib/gde
+                arbsrc*/lib/import
+                arbsrc*/lib/inputMasks
+                arbsrc*/lib/macros
+                arbsrc*/lib/motifHack
+                arbsrc*/lib/nas
+                arbsrc*/lib/pictures
+                arbsrc*/lib/pixmaps
+                arbsrc*/lib/rna3d
+                arbsrc*/lib/sellists
+                arbsrc*/lib/submit
+                arbsrc*/lib/LoVPBN.*
+                arbsrc*/lib/macro.head
                 arbsrc*/ptpan*
                 arbsrc*/util
 

debian/libarb-dev.links

+#!/usr/bin/dh-exec
 # Add symlink for tools expecting upstream non FHS location of header files
 usr/include/arb usr/lib/${DEB_HOST_MULTIARCH}/arb/INCLUDE
\ No newline at end of file

debian/libarb.install

 #!/usr/bin/dh-exec
 lib/*.so	usr/lib/${DEB_HOST_MULTIARCH}/arb
+lib/arb_tcp.dat	etc/arb

debian/libarb.links

+#!/usr/bin/dh-exec
 # ARB expects a folder $ARBHOME to contain lib/libARBDB.so
 usr/lib/${DEB_HOST_MULTIARCH}/arb	usr/lib/${DEB_HOST_MULTIARCH}/arb/lib
+etc/arb/arb_tcp.dat			usr/lib/${DEB_HOST_MULTIARCH}/arb/arb_tcp.dat

debian/rules

@@ -50,9 +50,9 @@ override_dh_auto_build:
 	ln -s ../SL/HELIX/BI_basepos.hxx INCLUDE/BI_basepos.hxx
 	ln -s ../SL/HELIX/BI_helix.hxx INCLUDE/BI_helix.hxx
 	mkdir bin
-	mkdir lib
 	dh_auto_build -- all # --sourcedirectory=CORE
 	make bin/arb_pt_server
+	cd lib && make tcpdat
 
 override_dh_auto_configure: config.makefile
 
@@ -64,7 +64,7 @@ override_dh_auto_clean: config.makefile
 	$(MAKE) clean
 	cd PROBE_COM; $(MAKE) clean; rm -f PT_*.h
 	rm -rf bin
-	rm -rf lib
+	rm -rf lib/lib*
 	rm -rf NAMES_COM
 	rm -rf PROBE_COM/AISC
 	rm -rf INCLUDE
@@ -72,6 +72,7 @@ override_dh_auto_clean: config.makefile
 	rm -rf AISC_MKPTPS/aisc_mkpt
 	rm -rf PROBE_COM/DUMP PROBE_COM/GENC PROBE_COM/GENH
 	rm config.makefile
+	rm -rf lib/arb_tcp.dat
 	# ARB does not have "distclean" or "realclean". Remove some leftovers:
 	rm -f UNIT_TESTER/Makefile.setup.local
 	find -name \*.log -a ! -name phyml-manual.log -print0 | xargs -0 rm -f

lib/GPL.txt

+
+Below is a copy of the GPL.  It does NOT apply to the ARB source code!
+
+It's only provided because ARB is distributed together with some GPLed
+software.  You can get the source of that software together with the
+ARB source code from http://arb-home.de/
+
+--------------------------------------------------------------------------------
+
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    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.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year  name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

lib/Makefile

+help.make:
+	@echo	'options'
+	@echo	'	nameserver		create nameserver from template'
+	@echo	'	tcpdat			create arb_tcp.dat from template'
+	@echo	''
+	@echo	'   all             all above'
+	@echo	'   clean           cleanup'
+
+all: tcpdat nameserver
+
+# ----------------------------------------
+# READ THIS!
+# 
+# Please be very careful here to NOT
+# touch the following files/directories if
+# they are links:
+# 
+#	./arb_tcp.dat
+#	./nas
+#	./pts
+#
+# ----------------------------------------
+
+tcpdat:
+	(	(test -e arb_tcp.dat || test -h arb_tcp.dat) \
+		&& echo "lib/arb_tcp.dat is a link - skipped" ) \
+		|| cp -p arb_tcp_org.dat arb_tcp.dat
+
+nameserver:
+	( test -h nas && echo "lib/nas is a link - skipped" ) || (cd nas;$(MAKE) all)
+
+clean:
+	rm -f *.so
+	( test -h nas && echo "lib/nas is a link - skipped" ) || (cd nas;$(MAKE) clean)
+	( test -h pts && echo "lib/pts is a link - skipped" ) || rm -rf pts
+	( test -h arb_tcp.dat && echo "lib/arb_tcp.dat is a link - skipped" ) || rm -f arb_tcp.dat

lib/arb_tcp_org.dat

+#*******************    Syntax ***********************************
+#
+#       [USER:]SERVER_ID                HOST:IP_NR      [programm       args]
+#       [USER:]SERVER_ID                :SOCKETPATH     [programm       args]
+#               [xxx] means optional field
+#               all $(enviroment_variable) are replaced by the value of the 'enviroment_variable'.
+#               if host is localhost then it is replaced by the result of `hostname`.
+#
+#   Specifying an username before the SERVER_ID makes the server user specific.
+#
+#   This file is searched at several locations:
+#       - in the current directory
+#       - in the $(HOME) (=home directory of the current user)
+#       - in $(ARBHOME)/lib
+#   The first occurrance found is taken.
+#
+#       Existing SERVER_IDs:
+#
+#               ARB_DB_SERVER               Your private database server. It is automatically started
+#               ARB_PT_SERVER               Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server)
+#               ARB_PT_SERVERn              Global PT_SERVERs. Needed for fast database search (align seq, probe des.)
+#                                                   n starts from 0 to max, no number can be excluded !!!
+#               ARB_NAME_SERVER             Generates short names for species (using 'acc')
+#               ARB_NAME_SERVER_field   Generates short names for species (using 'acc' and 'field')
+#
+#*****************************************************************
+
+# version of arb_tcp.dat
+ARB_TCP_DAT_VERSION 2
+
+#***********    Test Servers  ******************
+
+ARB_TEST_PT_SERVER          :$(ARBHOME)/UNIT_TESTER/sockets/pt.socket       arb_pt_server -D$(ARBHOME)/UNIT_TESTER/run/TEST_pt.arb
+ARB_TEST_PT_SERVER_GENE     :$(ARBHOME)/UNIT_TESTER/sockets/ptgene.socket  arb_pt_server -D$(ARBHOME)/UNIT_TESTER/run/TEST_gpt.arb
+
+#***********    Private Servers (for each user) ******************
+#
+# This is a local server, running on one machine. Each user has his own socket:
+# ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id
+# see programm $ARBHOME/SH/arb_clean to remove the sockets
+
+ARB_DB_SERVER           :/tmp/arb_db_$(USER)_$(ARB_PID)
+
+# If you want to run programs on a workstation cluster, you have to assign your arbdb server
+# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and
+# examine /etc/services whether this ip-id has not yet been allocated by another programm
+#       smith:ARB_DB_SERVER     myhost:4011             // socket for smith ('arb' has to be started on 'myhost')
+#       ludwig:ARB_DB_SERVER    myhost:4012             // socket for ludwig
+#       ARB_DB_SERVER           :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others
+
+#***********    Global Servers (for all users) ******************
+#
+#***********    Nameserver The server should run on the nfs server ******************
+# The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification
+#
+# You may define additional nameservers, using one additional field for identification.
+# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'.
+
+ARB_NAME_SERVER                 localhost:3020          arb_name_server -d$(ARBHOME)/lib/nas/names.dat
+ARB_NAME_SERVER_START           localhost:3021          arb_name_server -d$(ARBHOME)/lib/nas/names_start.dat -fstart=1
+# ARB_NAME_SERVER_STRAIN          localhost:3022          arb_name_server -d$(ARBHOME)/lib/nas/names_strain.dat -fstrain=
+# ARB_NAME_SERVER_POS_START       localhost:3023          arb_name_server -d$(ARBHOME)/lib/nas/names_pos_start.dat -fpos_start=1
+
+#***********    PT_SERVERS The server should run on the nfs server ******************
+#*******     You may add new pt_servers here: (numbers must be continued)   *********
+# Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not
+#       try to start/stop/update/... the server and will not check DB for existance.
+#       To use such a PT-Server you'll have to start it manually on the remote host
+
+ARB_PT_SERVER0          localhost:3030                       arb_pt_server   -D$(ARBHOME)/lib/pts/probe_server.arb
+ARB_PT_SERVER1          localhost:3031                       arb_pt_server   -D$(ARBHOME)/lib/pts/LSU_rRNA.arb
+ARB_PT_SERVER2          localhost:3032                       arb_pt_server   -D$(ARBHOME)/lib/pts/SSU_rRNA.arb
+ARB_PT_SERVER3          :$(HOME)/.arb_pts/$(USER)1.socket    arb_pt_server   -D$(HOME)/.arb_pts/$(USER)1.arb
+ARB_PT_SERVER4          :$(HOME)/.arb_pts/$(USER)2.socket    arb_pt_server   -D$(HOME)/.arb_pts/$(USER)2.arb
+ARB_PT_SERVER5          :$(HOME)/.arb_pts/$(USER)3.socket    arb_pt_server   -D$(HOME)/.arb_pts/$(USER)3.arb
+ARB_PT_SERVER6          localhost:3033                       arb_pt_server   -D$(ARBHOME)/lib/pts/user1.arb
+ARB_PT_SERVER7          localhost:3034                       arb_pt_server   -D$(ARBHOME)/lib/pts/user2.arb
+ARB_PT_SERVER8          localhost:3035                       arb_pt_server   -D$(ARBHOME)/lib/pts/user3.arb
+ARB_PT_SERVER9          localhost:3036                       arb_pt_server   -D$(ARBHOME)/lib/pts/user4.arb
+ARB_PT_SERVER10         localhost:3037                       arb_pt_server   -D$(ARBHOME)/lib/pts/user5.arb