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 <[email protected]>, 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 <[email protected]> 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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Upstream-Source: http://pubmlst.org/software/database/mlstdbnet/download +X-Debianized-By: Andreas Tille <[email protected]> +X-Packaged-Date: Tue, 13 Jan 2009 11:48:08 +0100 + +Files: debian/* +Copyright: 2009 Andreas Tille <[email protected]> +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 "$UPSTREAMTARBALL" + +# Delete old and unreproducible tweaked JalView jar because Upstream said: +# Date: Wed, 14 Jan 2009 07:54:21 +0000 +# From: Keith Jolley <[email protected]> +# To: Andreas Tille <[email protected]> +# +# The included jalview binary was modified quite a bit by Man-Suen Chan +# (author of mlstdb) and Michele Clamp (original author of JalView version +# 1). The functionality is not particularly useful and I've never liked +# the way it spawned a Java program anyway, so I'd be happy to see it left out. + +rm -rf "$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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
