[med-svn] r6706 - in trunk/packages/ncbi-blast-plus/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Thu Apr 28 16:06:50 UTC 2011
Author: osallou-guest
Date: 2011-04-28 16:06:44 +0000 (Thu, 28 Apr 2011)
New Revision: 6706
Added:
trunk/packages/ncbi-blast-plus/trunk/debian/dirs
trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus-dev.docs
trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
trunk/packages/ncbi-blast-plus/trunk/debian/postinst
trunk/packages/ncbi-blast-plus/trunk/debian/postrm
trunk/packages/ncbi-blast-plus/trunk/debian/watch
Removed:
trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.cron.d.ex
trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.default.ex
trunk/packages/ncbi-blast-plus/trunk/debian/watch.ex
Modified:
trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian
trunk/packages/ncbi-blast-plus/trunk/debian/README.source
trunk/packages/ncbi-blast-plus/trunk/debian/changelog
trunk/packages/ncbi-blast-plus/trunk/debian/control
trunk/packages/ncbi-blast-plus/trunk/debian/copyright
trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
trunk/packages/ncbi-blast-plus/trunk/debian/rules
Log:
add ncbi-blast-plus debian packaging stuff
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,6 +1,6 @@
-ncbi-blast-plus for Debian
---------------------------
+blast-plus for Debian
+---------------------
<possible notes regarding this package - if none, delete this file>
- -- Steffen Moeller <srigirish at evolbio.mpg.de> Thu, 02 Dec 2010 18:18:41 +0100
+ -- Olivier Sallou <osallou at irisa.fr> Wed, 27 Apr 2011 15:19:59 +0200
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/README.source
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/README.source 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/README.source 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,5 +1,5 @@
-ncbi-blast-plus for Debian
---------------------------
+blast-plus for Debian
+---------------------
<this file describes information about the source package, see Debian policy
manual section 4.14. You WILL either need to modify or delete this file>
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/changelog 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/changelog 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,5 +1,5 @@
-ncbi-blast-plus (2.2.24+-1) unstable; urgency=low
+ncbi-blast-plus (2.2.25-1) unstable; urgency=low
* Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
- -- Steffen Moeller <srigirish at evolbio.mpg.de> Thu, 02 Dec 2010 18:18:41 +0100
+ -- Olivier Sallou <osallou at irisa.fr> Wed, 27 Apr 2011 15:19:59 +0200
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,15 +1,33 @@
Source: ncbi-blast-plus
-Section: unknown
-Priority: extra
-Maintainer: Steffen Moeller <srigirish at evolbio.mpg.de>
-Build-Depends: debhelper (>= 7.0.50~)
-Standards-Version: 3.8.4
-Homepage: <insert the upstream URL, if relevant>
-#Vcs-Git: git://git.debian.org/collab-maint/ncbi-blast-plus.git
-#Vcs-Browser: http://git.debian.org/?p=collab-maint/ncbi-blast-plus.git;a=summary
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 7.0.50~),libboost-all-dev,zlib1g-dev,bzip2,python,libpcre++-dev,zlib1g-dev
+Standards-Version: 3.9.1
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>
+DM-Upload-Allowed: yes
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Homepage: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast-plus/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast-plus/?rev=0
+
Package: ncbi-blast-plus
Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},libboost-all-dev,ncbi-data,python,bzip2,libpcre++0, zlib1g
+Conflicts: blast2
+Description: NCBI Blast+ is new blast evolution
+ The Basic Local Alignment Search Tool (BLAST) is the most widely
+ used sequence similarity tool. There are versions of BLAST that
+ compare protein queries to protein databases, nucleotide queries
+ to nucleotide databases, as well as versions that translate nucleotide
+ queries or databases in all six frames and compare to protein databases or queries.
+ PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
+ with a protein query, and then uses that PSSM to perform further searches.
+ It is also possible to compare a protein or nucleotide query to a database of PSSM’s.
+ The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service.
+
+Package: ncbi-blast-plus-dev
+Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: <insert up to 60 chars description>
- <insert long description, indented with spaces>
+Description: Libraries and includes for development
+ Contains static libraries files and ncbi-tools++ includes.
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/copyright
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/copyright 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/copyright 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,37 +1,212 @@
-This work was packaged for Debian by:
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: ncbi-blast-plus
- Steffen Moeller <srigirish at evolbio.mpg.de> on Thu, 02 Dec 2010 18:18:41 +0100
+Files: src/util/regexp/*
+Copyright: 1997-2009 University of Cambridge
+2008-2009 Google Inc
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
-It was downloaded from:
+ 2. The origin of this software must not be misrepresented; you must
+ not claim that you wrote the original software. If you use this
+ software in a product, an acknowledgment in the product
+ documentation would be appreciated but is not required.
- <url://example.com>
+ 3. Altered source versions must be plainly marked as such, and must
+ not be misrepresented as being the original software.
-Upstream Author(s):
+ 4. The name of the author may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
- <put author's name and email here>
- <likewise for another author>
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Copyright:
- <Copyright (C) YYYY Firstname Lastname>
- <likewise for another author>
+Files: src/util/compress/bzip2/*
+Copyright: 1996-2002 Julian R Seward
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. The origin of this software must not be misrepresented; you must
+ not claim that you wrote the original software. If you use this
+ software in a product, an acknowledgment in the product
+ documentation would be appreciated but is not required.
+
+ 3. Altered source versions must be plainly marked as such, and must
+ not be misrepresented as being the original software.
+
+ 4. The name of the author may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+ GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: src/build-system/config.guess
+src/build-system/config.sub
+src/util/regexp/missing
+Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc
+License: GPLv2
+
+Files: src/build-system/ax_jni_include_dir.m4
+Copyright: 2008 Don Anderson <dda at sleepycat.com>
License:
+ Copying and distribution of this file, with or without modification, are
+ permitted in any medium without royalty provided the copyright notice
+ and this notice are preserved. This file is offered as-is, without any
+ warranty.
- <Put the license of the package here indented by 4 spaces>
+Files: scripts/projects/xmlwrapp/*
+Copyright: 2001-2003 Peter J Jones <pjones at pmade.org>
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.
+ 3. Neither the name of the Author nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS''
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR
+ OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
+ AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
-The Debian packaging is:
+Files: include/util/impl/floating_point_comparison.hpp
+Copyright: 2001-2008 Gennadiy Rozental
+License: Boost software license
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
- Copyright (C) 2010 Steffen Moeller <srigirish at evolbio.mpg.de>
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
-# Please chose a license for your packaging work. If the program you package
-# uses a mainstream license, using the same license is the safest choice.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
-# If you just want it to be GPL version 3, leave the following lines in.
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
-and is licensed under the GPL version 3,
-see "/usr/share/common-licenses/GPL-3".
+Files: include/dbapi/driver/odbc/unix_odbc/sqlfront.h
+Copyright: 1998-1999 Brian Bruns
+License: GPLv2
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
+Files: src/html/ncbi_menu_*.js
+Copyright: 1997-1999 Netscape Communications Corp.
+License: Netscape
+ Netscape grants you a royalty free license to use or modify this
+ software provided that this copyright notice appears on all copies.
+ This software is provided "AS IS," without a warranty of any kind.
+
+
+Files: include/util/bitset/*
+Copyright: 2002-2003 Anatoliy Kuznetsov
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, sublicense, and/or sell copies of the Software,
+ and to permit persons to whom the Software is furnished to do so,
+ subject to the following conditions:
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+Files: *
+Copyright: NCBI
+License: PD
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+
+ Please cite the author in any work or product based on this material.
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-2+
+ This package 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 package 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, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Added: trunk/packages/ncbi-blast-plus/trunk/debian/dirs
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/dirs (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/dirs 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1,2 @@
+usr/bin
+var/lib/ncbi-blast-plus/db
Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus-dev.docs
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus-dev.docs (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus-dev.docs 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1 @@
+include/util/bitset/license.txt
Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.cron.d.ex
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.cron.d.ex 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.cron.d.ex 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,4 +0,0 @@
-#
-# Regular cron jobs for the ncbi-blast-plus package
-#
-0 4 * * * root [ -x /usr/bin/ncbi-blast-plus_maintenance ] && /usr/bin/ncbi-blast-plus_maintenance
Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.default.ex
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.default.ex 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.default.ex 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,10 +0,0 @@
-# Defaults for ncbi-blast-plus initscript
-# sourced by /etc/init.d/ncbi-blast-plus
-# installed at /etc/default/ncbi-blast-plus by the maintainer scripts
-
-#
-# This is a POSIX shell fragment
-#
-
-# Additional options that are passed to the Daemon.
-DAEMON_OPTS=""
Added: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1,29 @@
+--- a/scripts/common/check/check_make_unix.sh
++++ b/scripts/common/check/check_make_unix.sh
+@@ -503,8 +503,8 @@
+ # Also, process guard works better if used after "time -p".
+ launch_sh="/var/tmp/launch.\$\$.sh"
+ cat > \$launch_sh <<EOF_launch
+-#! /bin/sh
+-exec time -p \$check_exec \`eval echo \$xx_run\`
++#! /bin/bash
++time -p \$check_exec \`eval echo \$xx_run\`
+ EOF_launch
+ chmod a+x \$launch_sh
+ \$launch_sh >\$x_log 2>&1
+--- a/src/serial/datatool/datatool.sh
++++ b/src/serial/datatool/datatool.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#! /bin/bash
+ # $Id: datatool.sh 79502 2006-03-23 19:45:38Z gouriano $
+ #
+
+--- a/src/serial/datatool/datatool_xml.sh
++++ b/src/serial/datatool/datatool_xml.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#! /bin/bash
+ # $Id: datatool_xml.sh 141084 2008-09-23 19:53:09Z ivanovp $
+ #
+
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/series 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/series 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1 +1 @@
-root_Makefile.patch
+fix_checks
Added: trunk/packages/ncbi-blast-plus/trunk/debian/postinst
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/postinst (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/postinst 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1,48 @@
+#!/bin/sh
+# postinst script for blast-plus
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postinst> `configure' <most-recently-configured-version>
+# * <old-postinst> `abort-upgrade' <new version>
+# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+# <new-version>
+# * <postinst> `abort-remove'
+# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+# <failed-install-package> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ configure)
+ echo "/usr/lib/ncbi-blast-plus" > /etc/ld.so.conf.d/ncbi-blast-plus.conf
+ ldconfig
+ #grep "BLASTDB" /etc/ncbi/.ncbirc >/dev/null
+ #if [ $? -eq 0 ];then
+ # echo "/etc/ncbi/.ncbirc already configured"
+ #else
+ # echo "[BLAST]\n" >> /etc/ncbi/.ncbirc
+ # echo "BLASTDB=/var/lib/ncbi-blast-plus/db\n" >> /etc/ncbi/.ncbirc
+ #fi
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/ncbi-blast-plus/trunk/debian/postrm
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/postrm (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/postrm 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1,41 @@
+#!/bin/sh
+# postrm script for blast-plus
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postrm> `remove'
+# * <postrm> `purge'
+# * <old-postrm> `upgrade' <new-version>
+# * <new-postrm> `failed-upgrade' <old-version>
+# * <new-postrm> `abort-install'
+# * <new-postrm> `abort-install' <old-version>
+# * <new-postrm> `abort-upgrade' <old-version>
+# * <disappearer's-postrm> `disappear' <overwriter>
+# <overwriter-version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ remove|purge)
+ rm /etc/ld.so.conf.d/ncbi-blast-plus.conf
+ ldconfig
+ ;;
+ upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-04-28 16:06:44 UTC (rev 6706)
@@ -9,17 +9,25 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-configure: configure.stamp
-configure.stamp:
- ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include
- touch $@
+export DEB_CONFIGURE_EXTRA_FLAGS= --with-dll --without-debug --with-mt --without-gbench --without-internal --libdir=${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus --bindir=${CURDIR}/debian/ncbi-blast-plus/usr/bin --includedir=${CURDIR}/debian/ncbi-blast-plus/usr/include
-build: build.stamp
-build.stamp: configure.stamp
- $(MAKE)
- touch $@
+override_dh_auto_configure:
+ mkdir -p ${CURDIR}/debian/tmp
+ ./configure ${DEB_CONFIGURE_EXTRA_FLAGS} --prefix=${CURDIR}/debian/ncbi-blast-plus
-#%:
-# dh $@
-.PHONY: configure
+override_dh_install:
+ dh_install
+ rm ${CURDIR}/debian/ncbi-blast-plus/usr/bin/*unit_test*
+ mkdir -p ${CURDIR}/debian/ncbi-blast-plus-dev/usr/lib/ncbi-blast-plus
+ mv ${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus/*.a ${CURDIR}/debian/ncbi-blast-plus-dev/usr/lib/ncbi-blast-plus/
+ #rm -rf ${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus
+ mv ${CURDIR}/debian/ncbi-blast-plus/usr/include ${CURDIR}/debian/ncbi-blast-plus-dev/usr/
+
+
+override_dh_clean:
+ dh_clean
+ find . -name ncbiconf_unix.h | xargs rm -f
+
+%:
+ dh $@
Added: trunk/packages/ncbi-blast-plus/trunk/debian/watch
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/watch (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/watch 2011-04-28 16:06:44 UTC (rev 6706)
@@ -0,0 +1,3 @@
+version=3
+opts=pasv,filenamemangle=s/\+-src/-orig/ \
+ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate
Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/watch.ex
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/watch.ex 2011-04-28 15:27:09 UTC (rev 6705)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/watch.ex 2011-04-28 16:06:44 UTC (rev 6706)
@@ -1,23 +0,0 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 3 file
-version=3
-
-# Uncomment to examine a Webpage
-# <Webpage URL> <string match>
-#http://www.example.com/downloads.php ncbi-blast-plus-(.*)\.tar\.gz
-
-# Uncomment to examine a Webserver directory
-#http://www.example.com/pub/ncbi-blast-plus-(.*)\.tar\.gz
-
-# Uncommment to examine a FTP server
-#ftp://ftp.example.com/pub/ncbi-blast-plus-(.*)\.tar\.gz debian uupdate
-
-# Uncomment to find new files on sourceforge, for devscripts >= 2.9
-# http://sf.net/ncbi-blast-plus/ncbi-blast-plus-(.*)\.tar\.gz
-
-# Uncomment to find new files on GooglePages
-# http://example.googlepages.com/foo.html ncbi-blast-plus-(.*)\.tar\.gz
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