Various changes explained in e-mail to list.

Remove need for tarball repackage
Work around conflict with blast2
Some other minor tweaks

diff --git a/debian/control b/debian/control
index 72731fafd184725758ca354521c87f77e0cec25b..ebdf10a7c5dcd694fd1c27a50ae5da6c81585fca 100644 (file)
--- 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 ce2802f26088c9386da33c7e70942bd84ba010f8..58c4486596c09c9fec365f08478861d793e5356d 100755 (executable)
--- 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 f1b82b27e897dae5d3346487fbe00e09328ebd35..06895c001e059164de5b8e3f9650233b2d31a26e 100644 (file)
--- 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 <olivier.sallou@irisa.fr>
 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 c34fb5f9a558470fd0bbb68e84d4291529a2fd36..a28de4eab5ef9526540659135d03e65d6b1710b3 100644 (file)
--- 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 <olivier.sallou@irisa.fr>
 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 e83b24692c490db8e84ad87b9075411695c0123a..9637e41db75592cd7c79d8da4e2de39373eb0535 100755 (executable)
--- 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