[med-svn] r17863 - in trunk/packages/arb/trunk/debian: . conf
Elmar Pruesse
epruesse-guest at moszumanska.debian.org
Wed Aug 27 17:39:59 UTC 2014
Author: epruesse-guest
Date: 2014-08-27 17:39:58 +0000 (Wed, 27 Aug 2014)
New Revision: 17863
Removed:
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
Modified:
trunk/packages/arb/trunk/debian/arb.install
Log:
use upstream's arb_tcp.dat
Modified: trunk/packages/arb/trunk/debian/arb.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb.install 2014-08-27 17:39:39 UTC (rev 17862)
+++ trunk/packages/arb/trunk/debian/arb.install 2014-08-27 17:39:58 UTC (rev 17863)
@@ -2,7 +2,7 @@
debian/bin/arb usr/bin
debian/bin/arb-kill usr/bin
debian/conf/arb.conf etc/arb
-debian/conf/arb_tcp.dat etc/arb
+debian/tmp/lib/arb_tcp.dat etc/arb
debian/tmp/bin usr/lib/arb
Deleted: trunk/packages/arb/trunk/debian/conf/arb_ntree.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_ntree.dat 2014-08-27 17:39:39 UTC (rev 17862)
+++ trunk/packages/arb/trunk/debian/conf/arb_ntree.dat 2014-08-27 17:39:58 UTC (rev 17863)
@@ -1,4 +0,0 @@
-#*********** 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
Deleted: trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat 2014-08-27 17:39:39 UTC (rev 17862)
+++ trunk/packages/arb/trunk/debian/conf/arb_pt_server.dat 2014-08-27 17:39:58 UTC (rev 17863)
@@ -1,27 +0,0 @@
-#*********** 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
Deleted: trunk/packages/arb/trunk/debian/conf/arb_tcp.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_tcp.dat 2014-08-27 17:39:39 UTC (rev 17862)
+++ trunk/packages/arb/trunk/debian/conf/arb_tcp.dat 2014-08-27 17:39:58 UTC (rev 17863)
@@ -1,89 +0,0 @@
-#******************* Syntax ***********************************
-#
-# [USER:]SERVER_ID HOST:IP_NR [programm args]
-# [USER:]SERVER_ID :SOCKETPATH [programm args]
-# [xxx] means optional field
-# all $(enviroment_variable) are replaced by the value of the 'enviroment_variable'.
-# if host is localhost then it is replaced by the result of `hostname`.
-#
-# Specifying an username before the SERVER_ID makes the server user specific.
-#
-# This file is searched at several locations:
-# - in the current directory
-# - in the $(HOME) (=home directory of the current user)
-# - in $(ARBHOME)/lib
-# The first occurrance found is taken.
-#
-# Existing SERVER_IDs:
-#
-# ARB_DB_SERVER Your private database server. It is automatically started
-# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server)
-# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.)
-# n starts from 0 to max, no number can be excluded !!!
-# ARB_NAME_SERVER Generates short names for species (using 'acc')
-# ARB_NAME_SERVER_field Generates short names for species (using 'acc' and 'field')
-#
-#*****************************************************************
-
-# version of arb_tcp.dat
-ARB_TCP_DAT_VERSION 2
-
-#*********** Private Servers (for each user) ******************
-#
-# This is a local server, running on one machine. Each user has his own socket:
-# ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id
-# see programm $ARBHOME/SH/arb_clean to remove the sockets
-
-ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID)
-
-# If you want to run programs on a workstation cluster, you have to assign your arbdb server
-# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and
-# examine /etc/services whether this ip-id has not yet been allocated by another programm
-# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' has to be started on 'myhost')
-# ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig
-# ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others
-
-#*********** Global Servers (for all users) ******************
-#
-#*********** Nameserver The server should run on the nfs server ******************
-# The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification
-#
-# You may define additional nameservers, using one additional field for identification.
-# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'.
-
-ARB_NAME_SERVER localhost:3020 arb_name_server -d/var/lib/arb/nas/names.dat
-ARB_NAME_SERVER_START localhost:3021 arb_name_server -d/var/lib/arb/nas/names_start.dat -fstart
-
-#*********** PT_SERVERS The server should run on the nfs server ******************
-#******* You may add new pt_servers here: (numbers must be continued) *********
-# Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not
-# try to start/stop/update/... the server and will not check DB for existance.
-# To use such a PT-Server you'll have to start it manually on the remote host
-#
-# FORMAT:
-# ARB_PT_SERVER<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/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
Deleted: trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat 2014-08-27 17:39:39 UTC (rev 17862)
+++ trunk/packages/arb/trunk/debian/conf/arb_tcp_template.dat 2014-08-27 17:39:58 UTC (rev 17863)
@@ -1,36 +0,0 @@
-#******************* 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) ******************
-#
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