[med-svn] r6784 - in trunk/packages/ncbi-blast-plus/trunk/debian: . patches

Timothy Booth tbooth-guest at alioth.debian.org
Fri May 6 07:53:52 UTC 2011 

Author: tbooth-guest
Date: 2011-05-06 07:53:50 +0000 (Fri, 06 May 2011)
New Revision: 6784

Modified:
   trunk/packages/ncbi-blast-plus/trunk/debian/control
   trunk/packages/ncbi-blast-plus/trunk/debian/get-orig-source
   trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
   trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error
   trunk/packages/ncbi-blast-plus/trunk/debian/rules
Log:
Various changes explained in e-mail to list.

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



Modified: trunk/packages/ncbi-blast-plus/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/control	2011-05-06 07:31:21 UTC (rev 6783)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/control	2011-05-06 07:53:50 UTC (rev 6784)
@@ -13,11 +13,10 @@
 
 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 @@
  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.

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/get-orig-source	2011-05-06 07:31:21 UTC (rev 6783)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/get-orig-source	2011-05-06 07:53:50 UTC (rev 6784)
@@ -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
-

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks	2011-05-06 07:31:21 UTC (rev 6783)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks	2011-05-06 07:53:50 UTC (rev 6784)
@@ -4,8 +4,8 @@
 
 Author: Olivier Sallou <olivier.sallou at 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 @@
  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

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error	2011-05-06 07:31:21 UTC (rev 6783)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error	2011-05-06 07:53:50 UTC (rev 6784)
@@ -5,8 +5,8 @@
 
 Author: Olivier Sallou <olivier.sallou at 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 @@
  
  
  // (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;
      

Modified: trunk/packages/ncbi-blast-plus/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/rules	2011-05-06 07:31:21 UTC (rev 6783)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/rules	2011-05-06 07:53:50 UTC (rev 6784)
@@ -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 @@
 	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

More information about the debian-med-commit mailing list