[med-svn] r2978 - in trunk/packages: . mlstdbnet mlstdbnet/trunk mlstdbnet/trunk/debian mlstdbnet/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Wed Jan 14 08:24:02 UTC 2009
Author: tille
Date: 2009-01-14 08:24:02 +0000 (Wed, 14 Jan 2009)
New Revision: 2978
Added:
trunk/packages/mlstdbnet/
trunk/packages/mlstdbnet/trunk/
trunk/packages/mlstdbnet/trunk/debian/
trunk/packages/mlstdbnet/trunk/debian/README.Debian
trunk/packages/mlstdbnet/trunk/debian/changelog
trunk/packages/mlstdbnet/trunk/debian/control
trunk/packages/mlstdbnet/trunk/debian/copyright
trunk/packages/mlstdbnet/trunk/debian/get-orig-source
trunk/packages/mlstdbnet/trunk/debian/patches/
trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
trunk/packages/mlstdbnet/trunk/debian/patches/series
trunk/packages/mlstdbnet/trunk/debian/watch
Log:
Inject first packaging stuff for mlstdbnet which fits our needs better than agdbnet
Added: trunk/packages/mlstdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/README.Debian 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,8 @@
+mlstdbnet for Debian
+--------------------
+
+Creating the database for MlstDbNet
+-----------------------------------
+
+
+ -- Andreas Tille <tillea at rki.de>, Wed, 24 Sep 2008 14:23:04 +0200
Added: trunk/packages/mlstdbnet/trunk/debian/changelog
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/changelog (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/changelog 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,5 @@
+mlstdbnet (2.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #??????)
+
+ -- Andreas Tille <tille at debian.org> Tue, 13 Jan 2009 11:48:08 +0100
Added: trunk/packages/mlstdbnet/trunk/debian/control
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/control (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/control 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,24 @@
+Source: mlstdbnet
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7), quilt, cdbs
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mlstdbnet/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mlstdbnet/trunk/
+Homepage: http://pubmlst.org/software/database/mlstdbnet/
+
+Package: mlstdbnet
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, blast2, postgresql-8.3,
+ libcgi-pm-perl, libdbd-pg-perl, libxml-perl, dbconfig-common, apache2,
+ imagemagic | graphicsmagic
+Recommends: libapache2-mod-perl2
+Description: mlst typing database
+ mlstdbNet is the software that drives the majority of publicly available
+ MLST databases, including those for Neisseria, the largest scheme available.
+ The software is derived from the original mlstdb package written by Man-Suen
+ Chan (Chan et al, 2001, Bioinformatics, 17, 1077-1083). This implementation
+ introduces significant improvements, allowing a distributed database structure.
Added: trunk/packages/mlstdbnet/trunk/debian/copyright
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/copyright (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/copyright 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,29 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Upstream-Name: mlstdbnet
+Upstream-Maintainer: Keith Jolley <keith.jolley at medawar.ox.ac.uk>
+Upstream-Source: http://pubmlst.org/software/database/mlstdbnet/download
+X-Debianized-By: Andreas Tille <tille at debian.org>
+X-Packaged-Date: Tue, 13 Jan 2009 11:48:08 +0100
+
+Files: debian/*
+Copyright: 2009 Andreas Tille <tille at debian.org>
+License: Same as mlstdbnet itself
+
+Files: *
+Copyright: (C) 2004-2006 Keith Jolley, University of Oxford
+ 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.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/mlstdbnet/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/get-orig-source 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+#set -x
+NAME=mlstdbnet
+UPSTREAMDIR=http://pubmlst.org/software/database/mlstdbnet/download
+
+version=`dpkg-parsechangelog | grep "^Version:" | sed -e "s/^Version:[[:space:]]\+\([.0-9]\+\)-.*/\1/"`
+UPSTREAMNAME=mlstdbnet_v"$version"
+UPSTREAMTARBALL="$UPSTREAMNAME".tar.gz
+
+mkdir -p ../tarballs
+cd ../tarballs
+wget -N "$UPSTREAMDIR"/"$UPSTREAMTARBALL"
+tar -xzf "$UPSTREAMTARBALL"
+
+# Delete old and unreproducible tweaked JalView jar because Upstream said:
+# Date: Wed, 14 Jan 2009 07:54:21 +0000
+# From: Keith Jolley <keith.jolley at zoo.ox.ac.uk>
+# To: Andreas Tille <tillea at rki.de>
+#
+# The included jalview binary was modified quite a bit by Man-Suen Chan
+# (author of mlstdb) and Michele Clamp (original author of JalView version
+# 1). The functionality is not particularly useful and I've never liked
+# the way it spawned a Java program anyway, so I'd be happy to see it left out.
+
+rm -rf "$UPSTREAMNAME"/java
+
+GZIP=-9 tar -czf "$NAME"_"$version".orig.tar.gz "$UPSTREAMNAME"
+rm -rf "$UPSTREAMNAME"
Added: trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,11 @@
+--- mlstdbnet_v2.0.0.orig/cgi-bin/mlstdbnet.pl
++++ mlstdbnet_v2.0.0/cgi-bin/mlstdbnet.pl
+@@ -54,7 +54,7 @@
+ ######################################################
+
+ ###########Local configuration########################
+-local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
++local ( our $configfile = '/etc/mlstdbnet/mlstdbnet.conf' );
+ #######End Local configuration########################
+
+ #######Lexically-scoped variables#####################
Added: trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,32 @@
+--- mlstdbnet_v2.0.0.orig/conf/mlstdbnet.conf
++++ mlstdbnet_v2.0.0/conf/mlstdbnet.conf
+@@ -1,11 +1,11 @@
+ ###GENERAL####
+-tmp_dir=/home/httpd/pubmlst.org/tmp
++tmp_dir=/var/www/mlstdbnet/temporary
+
+ ####EMBOSS####
+ #used for sequence alignment in allele query
+ #set 'emboss=0' to remove functionality
+ emboss=1
+-emboss_path=/usr/local/bin
++emboss_path=/usr/lib/emboss
+
+ ####JALVIEW####
+ #used for global sequence alignment in allele query
+@@ -21,7 +21,7 @@
+ #Used for databases where sequences are of unequal
+ #length
+ blast=1
+-blast_path=/usr/local/blast/bin
++blast_path=/usr/bin
+
+ ##REFERENCE DB#
+ #Set to 1 if you have set up a local reference database.
+@@ -77,4 +77,4 @@
+ #suggest a bug and should be reported.
+ debug=0
+ #BENCHMARKING#
+-debug_timing=0
+\ No newline at end of file
++debug_timing=0
Added: trunk/packages/mlstdbnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/series 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,2 @@
+10_preconf.patch
+10_config_location.patch
Added: trunk/packages/mlstdbnet/trunk/debian/watch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/watch (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/watch 2009-01-14 08:24:02 UTC (rev 2978)
@@ -0,0 +1,2 @@
+version=3
+http://pubmlst.org/software/database/mlstdbnet/download/mlstdbnet_v([\d.]+)\.tar\.gz
More information about the debian-med-commit
mailing list