[med-svn] r876 - in trunk/packages/arb/trunk/debian: . conf patches
tille at alioth.debian.org
tille at alioth.debian.org
Sun Dec 2 19:59:09 UTC 2007
Author: tille
Date: 2007-12-02 19:59:08 +0000 (Sun, 02 Dec 2007)
New Revision: 876
Removed:
trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch
trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch
Modified:
trunk/packages/arb/trunk/debian/arb.README.debian
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/conf/arb_tcp.dat
trunk/packages/arb/trunk/debian/get-orig-source
trunk/packages/arb/trunk/debian/patches/00list
trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch
Log:
New upstream version
Modified: trunk/packages/arb/trunk/debian/arb.README.debian
===================================================================
--- trunk/packages/arb/trunk/debian/arb.README.debian 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/arb.README.debian 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,6 +1,10 @@
Arb for DEBIAN
--------------
+Known bugs of arb are listed in the bug-tracker at
+ http://bugs.arb-home.de/
+
+
The FTP archive where this version was downloaded from says:
+---------------------------------------------------------------------------------+
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/changelog 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,4 +1,4 @@
-arb (0.0.20071029-1) unstable; urgency=low
+arb (0.0.20071120-1) unstable; urgency=low
* New upstream version
Closes: #446666
Modified: trunk/packages/arb/trunk/debian/conf/arb_tcp.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_tcp.dat 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/conf/arb_tcp.dat 2007-12-02 19:59:08 UTC (rev 876)
@@ -3,19 +3,30 @@
# [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`
+# 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 $(ARBHOME)/lib
+# The first occurrance found is taken.
+#
# Existing SERVER_IDs:
#
-# ARB_DB_SERVER Your private database server. It is automatically started
-# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server)
-# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.)
-# n starts from 0 to max, no number can be excluded !!!
-# ARB_NAME_SERVER Generates short names for species
+# ARB_DB_SERVER Your private database server. It is automatically started
+# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server)
+# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.)
+# n starts from 0 to max, no number can be excluded !!!
+# ARB_NAME_SERVER Generates short names for species (using 'acc')
+# ARB_NAME_SERVER_field Generates short names for species (using 'acc' and 'field')
#
#*****************************************************************
+# version of arb_tcp.dat
+ARB_TCP_DAT_VERSION 2
#*********** Private Servers (for each user) ******************
#
@@ -28,21 +39,29 @@
# If you want to run programs on a workstation cluster, you have to assign your arbdb server
# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and
# examine /etc/services whether this ip-id has not yet been allocated by another programm
-# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' have to be started on 'myhost')
+# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' has to be started on 'myhost')
# ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig
# ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others
#*********** Global Servers (for all users) ******************
#
#*********** Nameserver The server should run on the nfs server ******************
+# The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification
+#
+# You may define additional nameservers, using one additional field for identification.
+# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'.
-## This is the Debian location for ARB name server
-ARB_NAME_SERVER localhost:3029 arb_name_server -d/var/lib/arb/nas/names.dat
+ARB_NAME_SERVER localhost:3020 arb_name_server -d/var/lib/arb/lib/nas/names.dat
+ARB_NAME_SERVER_START localhost:3021 arb_name_server -d/var/lib/arb/lib/nas/names_start.dat -fstart
+
#*********** PT_SERVERS The server should run on the nfs server ******************
-#******* You may add new pt_servers here: (numbers must be continues) *********
-
+#******* You may add new pt_servers here: (numbers must be continued) *********
+# Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not
+# try to start/stop/update/... the server and will not check DB for existance.
+# To use such a PT-Server you'll have to start it manually on the remote host
+#
# FORMAT:
-# ARB_PT_SERVER<n> localhost:303<n> arb_pt_server -D<path_to_arb_database>
+# ARB_PT_SERVER<n> localhost:303<n> arb_pt_server -D<path_to_arb_database>
# where <n> is a integer number increased by one according to the entry before
# path_to_arb_database is the location of the database file
#
@@ -55,13 +74,16 @@
# The following database is shipped with the package arb-database
# Further versions will add this in the postinst script but this is left
# here for the process of beta testing.
-ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb
+ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb
-# Examples:
-#ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(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
+# Examples
+#ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/LSU_rRNA.arb
+#ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/SSU_rRNA.arb
+#ARB_PT_SERVER3 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb
+#ARB_PT_SERVER4 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb
+#ARB_PT_SERVER5 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/user3.arb
+#ARB_PT_SERVER6 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/user4.arb
+#ARB_PT_SERVER7 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/user5.arb
+#ARB_PT_SERVER8 localhost:3038 arb_pt_server -D$(ARBHOME)/lib/pts/user6.arb
+#ARB_PT_SERVER9 localhost:3039 arb_pt_server -D$(ARBHOME)/lib/pts/user7.arb
+#ARB_PT_SERVER10 localhost:3040 arb_pt_server -D$(ARBHOME)/lib/pts/user8.arb
Modified: trunk/packages/arb/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/arb/trunk/debian/get-orig-source 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/get-orig-source 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,23 +1,27 @@
#!/bin/sh -e
+set -e
+set -x
NAME=arb
UTARBALL=${NAME}src.tgz
downloadurl=http://www2.mikro.biologie.tu-muenchen.de/download/ARB/latest_build/
RemoveFilesFromSource="GDEHELP/HELP_DOC_GEN/* GDEHELP/HELP_GEN/* GDEHELP/ARB_GDEmenus GDEHELP/helpfiles.lst HELP_SOURCE/_index.html NTREE/nt_date.h lib/ARB.pm"
+TMPDIR=../tarballs
+mkdir -p "$TMPDIR"
+cd "$TMPDIR"
+
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 ../../"$UTARBALL"
+VERSION=`ls -lt "$UTARBALL" | 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/'`
+mkdir -p arbdir
+cd 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"
@@ -41,6 +45,4 @@
GZIP=-9 tar -czf "$NAME"_"$VERSION".orig.tar.gz "$NAME"-"$VERSION"
-mv "$NAME"_"$VERSION".orig.tar.gz ..
-cd ..
-rm -rf tmp
+rm -rf "$NAME"-"$VERSION"
Modified: trunk/packages/arb/trunk/debian/patches/00list
===================================================================
--- trunk/packages/arb/trunk/debian/patches/00list 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/patches/00list 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,5 +1,3 @@
20_config.makefiles.dpatch
-20_developer_tools.dpatch
20_Makefiles.dpatch
-20_perl_scripts.dpatch
30_Makefile_main.dpatch
Modified: trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles.dpatch 2007-12-02 19:59:08 UTC (rev 876)
@@ -39,18 +39,6 @@
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 $(GCC) -dumpversion)
diff -urbN arb-0.0.20071029.orig/NAMES_COM/Makefile arb-0.0.20071029/NAMES_COM/Makefile
--- arb-0.0.20071029.orig/NAMES_COM/Makefile 2007-06-29 21:04:04.000000000 +0200
+++ arb-0.0.20071029/NAMES_COM/Makefile 2007-09-12 15:59:27.000000000 +0200
Deleted: trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/patches/20_developer_tools.dpatch 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,23 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 20_developer_tools.dpatch by <tille at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: This tool seems to be only interesting for developers of Arb. Because
-## DP: this fact is not documented it is installed with the package but needs
-## DP: fixing.
-
- at DPATCH@
-
-diff -urbN arb-0.0.20071029.orig/util/arb_export arb-0.0.20071029/util/arb_export
---- arb-0.0.20071029.orig/util/arb_export 2003-08-22 23:07:55.000000000 +0200
-+++ arb-0.0.20071029/util/arb_export 2005-10-07 08:19:30.000000000 +0200
-@@ -28,6 +28,6 @@
- # export names.dat:
- echo "****************************************"
- echo "exporting names.dat"
--echo gzip </usr/arb/lib/nas/names.dat >$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
Deleted: trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch 2007-12-02 17:24:08 UTC (rev 875)
+++ trunk/packages/arb/trunk/debian/patches/20_perl_scripts.dpatch 2007-12-02 19:59:08 UTC (rev 876)
@@ -1,17 +0,0 @@
-#! /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 #
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