From: Olivier Sallou Date: Thu, 28 Apr 2011 16:06:44 +0000 (+0000) Subject: add ncbi-blast-plus debian packaging stuff X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~381 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=32393f15082f54e288ac4dd9bf1ef49fdd771221;p=ncbi-blast%2B.git add ncbi-blast-plus debian packaging stuff --- diff --git a/debian/README.Debian b/debian/README.Debian index a3cd3b36..34b40883 100644 --- a/debian/README.Debian +++ b/debian/README.Debian @@ -1,6 +1,6 @@ -ncbi-blast-plus for Debian --------------------------- +blast-plus for Debian +--------------------- - -- Steffen Moeller Thu, 02 Dec 2010 18:18:41 +0100 + -- Olivier Sallou Wed, 27 Apr 2011 15:19:59 +0200 diff --git a/debian/README.source b/debian/README.source index 0c50f26b..02dfd898 100644 --- a/debian/README.source +++ b/debian/README.source @@ -1,5 +1,5 @@ -ncbi-blast-plus for Debian --------------------------- +blast-plus for Debian +--------------------- diff --git a/debian/changelog b/debian/changelog index 6c50156a..ba6fc109 100644 --- a/debian/changelog +++ b/debian/changelog @@ -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) - -- Steffen Moeller Thu, 02 Dec 2010 18:18:41 +0100 + -- Olivier Sallou Wed, 27 Apr 2011 15:19:59 +0200 diff --git a/debian/control b/debian/control index 5dc165e2..fc438cd7 100644 --- a/debian/control +++ b/debian/control @@ -1,15 +1,33 @@ Source: ncbi-blast-plus -Section: unknown -Priority: extra -Maintainer: Steffen Moeller -Build-Depends: debhelper (>= 7.0.50~) -Standards-Version: 3.8.4 -Homepage: -#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 +DM-Upload-Allowed: yes +Maintainer: Debian Med Packaging Team +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: - +Description: Libraries and includes for development + Contains static libraries files and ncbi-tools++ includes. diff --git a/debian/copyright b/debian/copyright index 47b25e31..bce93797 100644 --- a/debian/copyright +++ b/debian/copyright @@ -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 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. - + 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. - - + 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: - - +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 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. + +Files: scripts/projects/xmlwrapp/* +Copyright: 2001-2003 Peter J Jones +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. + +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: + + 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. + + 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. + +Files: include/dbapi/driver/odbc/unix_odbc/sqlfront.h +Copyright: 1998-1999 Brian Bruns +License: GPLv2 + +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 -The Debian packaging is: + 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. - Copyright (C) 2010 Steffen Moeller + 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 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. + Please cite the author in any work or product based on this material. -and is licensed under the GPL version 3, -see "/usr/share/common-licenses/GPL-3". +Files: debian/* +Copyright: 2011 Olivier Sallou +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 + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". -# Please also look if there are files or directories which have a -# different copyright/license attached and list them here. diff --git a/debian/dirs b/debian/dirs new file mode 100644 index 00000000..72d38d5d --- /dev/null +++ b/debian/dirs @@ -0,0 +1,2 @@ +usr/bin +var/lib/ncbi-blast-plus/db diff --git a/debian/ncbi-blast-plus-dev.docs b/debian/ncbi-blast-plus-dev.docs new file mode 100644 index 00000000..19923d64 --- /dev/null +++ b/debian/ncbi-blast-plus-dev.docs @@ -0,0 +1 @@ +include/util/bitset/license.txt diff --git a/debian/ncbi-blast-plus.cron.d.ex b/debian/ncbi-blast-plus.cron.d.ex deleted file mode 100644 index 27422e81..00000000 --- a/debian/ncbi-blast-plus.cron.d.ex +++ /dev/null @@ -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 diff --git a/debian/ncbi-blast-plus.default.ex b/debian/ncbi-blast-plus.default.ex deleted file mode 100644 index 874bc825..00000000 --- a/debian/ncbi-blast-plus.default.ex +++ /dev/null @@ -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="" diff --git a/debian/patches/fix_checks b/debian/patches/fix_checks new file mode 100644 index 00000000..bfdbc51f --- /dev/null +++ b/debian/patches/fix_checks @@ -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 <\$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 $ + # + diff --git a/debian/patches/series b/debian/patches/series index ee758d34..45ff98b8 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1 @@ -root_Makefile.patch +fix_checks diff --git a/debian/postinst b/debian/postinst new file mode 100644 index 00000000..6e3d2dea --- /dev/null +++ b/debian/postinst @@ -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: +# * `configure' +# * `abort-upgrade' +# * `abort-remove' `in-favour' +# +# * `abort-remove' +# * `abort-deconfigure' `in-favour' +# `removing' +# +# 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 diff --git a/debian/postrm b/debian/postrm new file mode 100644 index 00000000..51f4f42c --- /dev/null +++ b/debian/postrm @@ -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: +# * `remove' +# * `purge' +# * `upgrade' +# * `failed-upgrade' +# * `abort-install' +# * `abort-install' +# * `abort-upgrade' +# * `disappear' +# +# 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 \`$1'" >&2 + exit 1 + ;; +esac + +# dh_installdeb will replace this with shell code automatically +# generated by other debhelper scripts. + +#DEBHELPER# + +exit 0 diff --git a/debian/rules b/debian/rules index bd86dc34..0cdbf877 100755 --- a/debian/rules +++ b/debian/rules @@ -9,17 +9,25 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -configure: configure.stamp -configure.stamp: - ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${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 $@ diff --git a/debian/watch b/debian/watch new file mode 100644 index 00000000..ac0075ca --- /dev/null +++ b/debian/watch @@ -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 diff --git a/debian/watch.ex b/debian/watch.ex deleted file mode 100644 index fa81ed70..00000000 --- a/debian/watch.ex +++ /dev/null @@ -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 -# -#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