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 <[email protected]>
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 <[email protected]>
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
_______________________________________________
debian-med-commit mailing list
[email protected]
http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
