From 623843540f71b59010df52fd3c76420bd4fdff26 Mon Sep 17 00:00:00 2001 From: Tim Booth Date: Fri, 6 May 2011 07:53:50 +0000 Subject: [PATCH] Various changes explained in e-mail to list. Remove need for tarball repackage Work around conflict with blast2 Some other minor tweaks --- debian/control | 9 ++++----- debian/get-orig-source | 20 +------------------- debian/patches/fix_checks | 12 ++++++------ debian/patches/fix_gcc46_include_error | 8 ++++---- debian/rules | 12 ++++++++---- 5 files changed, 23 insertions(+), 38 deletions(-) diff --git a/debian/control b/debian/control index 72731faf..ebdf10a7 100644 --- a/debian/control +++ b/debian/control @@ -13,11 +13,10 @@ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast-plu Package: ncbi-blast-plus Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends},${perl:Depends},ncbi-data,bzip2,libpcre3,libpcre++0, zlib1g,python,perl,libboost-all -Conflicts: blast2 -Description: NCBI Blast+ is new blast evolution +Depends: ${shlibs:Depends}, ${misc:Depends},${perl:Depends},ncbi-data,bzip2,libpcre3,libpcre++0,zlib1g,python,libboost-all +Description: The next generation suite of BLAST sequence search tools The Basic Local Alignment Search Tool (BLAST) is the most widely - used sequence similarity tool. There are versions of BLAST that + 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 @@ -27,4 +26,4 @@ Description: NCBI Blast+ is new blast evolution 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. + a network service. diff --git a/debian/get-orig-source b/debian/get-orig-source index ce2802f2..58c44865 100755 --- a/debian/get-orig-source +++ b/debian/get-orig-source @@ -2,24 +2,6 @@ set -e -PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` -VERSION=`uscan --rename --verbose --force-download | - grep "Newest version on remote site is .* local version is .*" | - head -n 1 | - sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` +uscan --rename --verbose --force-download -mkdir -p ../tarballs -cd ../tarballs - -UTAR="${PKG}_${VERSION}.orig.tar.gz" -mv ../${UTAR} . -tar -xzf ${UTAR} - -mv ncbi-blast-${VERSION}+-src/c++ $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2 -rmdir ncbi-blast-${VERSION}+-src - -rm $UTAR - -BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig -rm -rf ${PKG}-${VERSION}.orig diff --git a/debian/patches/fix_checks b/debian/patches/fix_checks index f1b82b27..06895c00 100644 --- a/debian/patches/fix_checks +++ b/debian/patches/fix_checks @@ -4,8 +4,8 @@ Subject: command time not found when using shell Author: Olivier Sallou Last-Update: 2011-05-03 ---- a/scripts/common/check/check_make_unix.sh -+++ b/scripts/common/check/check_make_unix.sh +--- a/c++/scripts/common/check/check_make_unix.sh ++++ b/c++/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" @@ -17,16 +17,16 @@ Last-Update: 2011-05-03 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 +--- a/c++/src/serial/datatool/datatool.sh ++++ b/c++/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 +--- a/c++/src/serial/datatool/datatool_xml.sh ++++ b/c++/src/serial/datatool/datatool_xml.sh @@ -1,4 +1,4 @@ -#! /bin/sh +#! /bin/bash diff --git a/debian/patches/fix_gcc46_include_error b/debian/patches/fix_gcc46_include_error index c34fb5f9..a28de4ea 100644 --- a/debian/patches/fix_gcc46_include_error +++ b/debian/patches/fix_gcc46_include_error @@ -5,8 +5,8 @@ Subject: GCC 4.6 compilation error due to missing def Author: Olivier Sallou Last-Update: 2011-05-03 ---- a/include/corelib/ncbistre.hpp -+++ b/include/corelib/ncbistre.hpp +--- a/c++/include/corelib/ncbistre.hpp ++++ b/c++/include/corelib/ncbistre.hpp @@ -116,6 +116,7 @@ #define SEEKOFF PUBSEEKOFF @@ -15,8 +15,8 @@ Last-Update: 2011-05-03 // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file) ---- a/src/objtools/blast/seqdb_reader/seqdbimpl.hpp -+++ b/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp ++++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp @@ -1245,7 +1245,7 @@ CSeqDBAtlasHolder m_AtlasHolder; diff --git a/debian/rules b/debian/rules index e83b2469..9637e41d 100755 --- a/debian/rules +++ b/debian/rules @@ -9,13 +9,17 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -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=${CURDIR}/debian/ncbi-blast-plus/usr/include --with-3psw=std:netopt --without-dbapi +SOURCEDIR=${CURDIR}/c++ +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=$(SOURCEDIR)/include --with-3psw=std:netopt --without-dbapi override_dh_auto_configure: - ${CURDIR}/configure ${DEB_CONFIGURE_EXTRA_FLAGS} --prefix=${CURDIR}/debian/ncbi-blast-plus + ( cd $(SOURCEDIR) ; ./configure ${DEB_CONFIGURE_EXTRA_FLAGS} --prefix=${SOURCEDIR}/debian/ncbi-blast-plus ) override_dh_install: + #TODO - can I just use -X.a -Xinclude instead of removing unneeded files later? dh_install rm -f ${CURDIR}/debian/ncbi-blast-plus/usr/bin/*test* #mkdir -p ${CURDIR}/debian/ncbi-blast-plus-dev/usr/lib/ncbi-blast-plus @@ -25,14 +29,14 @@ override_dh_install: rm -rf ${CURDIR}/debian/ncbi-blast-plus/usr/include find ${CURDIR}/debian/ncbi-blast-plus/usr/bin/ -type f -not -name "*.p*" | xargs chrpath -d find ${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus/*.so | xargs chrpath -d + mv ${CURDIR}/debian/ncbi-blast-plus/usr/bin/rpsblast ${CURDIR}/debian/ncbi-blast-plus/usr/bin/rpsblast+ override_dh_clean: dh_clean find . -name ncbiconf_unix.h | xargs rm -f %: - dh $@ - + dh $@ --with quilt --sourcedir=$(SOURCEDIR) get-orig-source: . debian/get-orig-source -- 2.30.2