Author: osallou-guest Date: 2011-05-09 11:48:10 +0000 (Mon, 09 May 2011) New Revision: 6795
Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.1 trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.manpages Removed: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1 trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages Modified: trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian trunk/packages/ncbi-blast-plus/trunk/debian/README.source trunk/packages/ncbi-blast-plus/trunk/debian/changelog trunk/packages/ncbi-blast-plus/trunk/debian/control trunk/packages/ncbi-blast-plus/trunk/debian/copyright trunk/packages/ncbi-blast-plus/trunk/debian/dirs trunk/packages/ncbi-blast-plus/trunk/debian/postinst trunk/packages/ncbi-blast-plus/trunk/debian/postrm trunk/packages/ncbi-blast-plus/trunk/debian/rules trunk/packages/ncbi-blast-plus/trunk/debian/watch Log: rename packages to blast+, update copyright for zlib, use libbooost-test instead of all Modified: trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/README.Debian 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,7 +1,7 @@ -blast-plus for Debian +blast+ for Debian --------------------- This package does not include the documentation of the software. Documentation is available online. - Detail is available: man ncbi-blast-plus + Detail is available: man ncbi-blast+ -- Olivier Sallou <[email protected]> Wed, 27 Apr 2011 15:19:59 +0200 Modified: trunk/packages/ncbi-blast-plus/trunk/debian/README.source =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/README.source 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/README.source 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,4 +1,4 @@ -blast-plus for Debian +blast+ for Debian --------------------- get-orig-source target downloads file via uscan and rearrange the package. Modified: trunk/packages/ncbi-blast-plus/trunk/debian/changelog =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/changelog 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/changelog 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,4 +1,4 @@ -ncbi-blast-plus (2.2.25-1) unstable; urgency=low +ncbi-blast+ (2.2.25-1) unstable; urgency=low * Initial release (Closes: #624394) Modified: trunk/packages/ncbi-blast-plus/trunk/debian/control =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,7 +1,7 @@ -Source: ncbi-blast-plus +Source: ncbi-blast+ Section: science Priority: optional -Build-Depends: debhelper (>= 7.0.50~),autotools-dev,zlib1g,bzip2,libbz2-dev,libpcre++-dev,libpcre3,zlib1g-dev,chrpath,libboost-all-dev,cpio +Build-Depends: debhelper (>= 7.0.50~),autotools-dev,zlib1g,bzip2,libbz2-dev,libpcre++-dev,libpcre3,zlib1g-dev,chrpath,libboost-test-dev,cpio Standards-Version: 3.9.1 Uploaders: Olivier Sallou <[email protected]> DM-Upload-Allowed: yes @@ -11,9 +11,9 @@ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast-plus/?rev=0 -Package: ncbi-blast-plus +Package: ncbi-blast+ Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends},${perl:Depends},ncbi-data,bzip2,libpcre3,libpcre++0,zlib1g,python,libboost-all +Depends: ${shlibs:Depends}, ${misc:Depends},${perl:Depends},ncbi-data,bzip2,libpcre3,libpcre++0,zlib1g,python 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 Modified: trunk/packages/ncbi-blast-plus/trunk/debian/copyright =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/copyright 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/copyright 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,6 +1,25 @@ Format: http://dep.debian.net/deps/dep5 -Upstream-Name: ncbi-blast-plus +Upstream-Name: ncbi-blast+ +Files: src/util/compress/zlib/* +Copyright: 1995-2004 Jean-loup Gailly and Mark Adler +License: + This software is provided 'as-is', without any express or implied + warranty. In no event will the authors be held liable for any damages + arising from the use of this software. + + Permission is granted to anyone to use this software for any purpose, + including commercial applications, and to alter it and redistribute it + freely, subject to the following restrictions: + + 1. 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. + 2. Altered source versions must be plainly marked as such, and must not be + misrepresented as being the original software. + 3. This notice may not be removed or altered from any source distribution. + Files: src/util/regexp/* Copyright: 1997-2009 University of Cambridge 2008-2009 Google Inc Modified: trunk/packages/ncbi-blast-plus/trunk/debian/dirs =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/dirs 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/dirs 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,2 +1,2 @@ usr/bin -var/lib/ncbi-blast-plus/db +var/lib/ncbi-blast+/db Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.1 =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.1 (rev 0) +++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.1 2011-05-09 11:48:10 UTC (rev 6795) @@ -0,0 +1,33 @@ +.TH ncbi-blast+ 1 "April 29, 2011" "version 2.2.25" "USER COMMANDS" +.SH NAME +ncbi-blast+ \- NCBI command tools for BLAST+ +.SH ONELINE DOCUMENTATION +.B BLAST+ documentation is available online at http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.PP +.SH DESCRIPTION +The NCBI BLAST+ is a group of tools for basic alignment search. BLAST+ + is a rewrite of BLAST with new features and performance improvements. +BLAST+ commands differ from original BLAST. For BLAST users, one should read + the BLAST USERS paragraph. +.PP +.SH CONFIGURATION +BLAST+ uses the BLASTDB environment variable to get default db directory. +It is possible to update the file /etc/ncbi/.ncbirc to add the following: +.B [BLAST] +.B BLASTDB=/var/lib/ncbi-blast+/db +.SH BLAST USERS +The easiest way to get started using these command line applications is + by means of the legacy_blast.pl PERL script which is bundled along with + the BLAST+ applications. +To utilize this script, simply prefix it to the invocation of the C toolkit + BLAST command line application and append the --path option pointing to the +installation directory of the BLAST+ applications. For example, instead of using + +.B blastall -i query -d nr -o blast.out +use +.B legacy_blast.pl blastall -i query -d nr -o blast.out --path /usr/bin + +.PP +.SH AUTHOR +Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging +NCBI - BLAST+ Added: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.manpages =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.manpages (rev 0) +++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast+.manpages 2011-05-09 11:48:10 UTC (rev 6795) @@ -0,0 +1 @@ +debian/*.1 Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1 =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.1 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,33 +0,0 @@ -.TH ncbi-blast-plus 1 "April 29, 2011" "version 2.2.25" "USER COMMANDS" -.SH NAME -ncbi-blast-plus \- NCBI command tools for BLAST+ -.SH ONELINE DOCUMENTATION -.B BLAST+ documentation is available online at http://www.ncbi.nlm.nih.gov/books/NBK1763/ -.PP -.SH DESCRIPTION -The NCBI BLAST+ is a group of tools for basic alignment search. BLAST+ - is a rewrite of BLAST with new features and performance improvements. -BLAST+ commands differ from original BLAST. For BLAST users, one should read - the BLAST USERS paragraph. -.PP -.SH CONFIGURATION -BLAST+ uses the BLASTDB environment variable to get default db directory. -It is possible to update the file /etc/ncbi/.ncbirc to add the following: -.B [BLAST] -.B BLASTDB=/var/lib/ncbi-blast-plus/db -.SH BLAST USERS -The easiest way to get started using these command line applications is - by means of the legacy_blast.pl PERL script which is bundled along with - the BLAST+ applications. -To utilize this script, simply prefix it to the invocation of the C toolkit - BLAST command line application and append the --path option pointing to the -installation directory of the BLAST+ applications. For example, instead of using - -.B blastall -i query -d nr -o blast.out -use -.B legacy_blast.pl blastall -i query -d nr -o blast.out --path /usr/bin - -.PP -.SH AUTHOR -Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging -NCBI - BLAST+ Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/ncbi-blast-plus.manpages 2011-05-09 11:48:10 UTC (rev 6795) @@ -1 +0,0 @@ -debian/*.1 Modified: trunk/packages/ncbi-blast-plus/trunk/debian/postinst =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/postinst 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/postinst 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,5 +1,5 @@ #!/bin/sh -# postinst script for blast-plus +# postinst script for blast+ # # see: dh_installdeb(1) @@ -20,14 +20,14 @@ case "$1" in configure) - echo "/usr/lib/ncbi-blast-plus" > /etc/ld.so.conf.d/ncbi-blast-plus.conf + echo "/usr/lib/ncbi-blast+" > /etc/ld.so.conf.d/ncbi-blast+.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 + # echo "BLASTDB=/var/lib/ncbi-blast+/db\n" >> /etc/ncbi/.ncbirc #fi ;; Modified: trunk/packages/ncbi-blast-plus/trunk/debian/postrm =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/postrm 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/postrm 2011-05-09 11:48:10 UTC (rev 6795) @@ -21,7 +21,7 @@ case "$1" in remove|purge) - rm /etc/ld.so.conf.d/ncbi-blast-plus.conf + rm /etc/ld.so.conf.d/ncbi-blast+.conf ldconfig ;; upgrade|failed-upgrade|abort-install|abort-upgrade|disappear) Modified: trunk/packages/ncbi-blast-plus/trunk/debian/rules =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-05-09 11:48:10 UTC (rev 6795) @@ -11,25 +11,25 @@ SOURCEDIR=${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 \ + --libdir=${CURDIR}/debian/ncbi-blast+/usr/lib/ncbi-blast+ --bindir=${CURDIR}/debian/ncbi-blast+/usr/bin \ --includedir=$(SOURCEDIR)/include --with-3psw=std:netopt --without-dbapi override_dh_auto_configure: - ( cd $(SOURCEDIR) ; ./configure ${DEB_CONFIGURE_EXTRA_FLAGS} --prefix=${SOURCEDIR}/debian/ncbi-blast-plus ) + ( cd $(SOURCEDIR) ; ./configure ${DEB_CONFIGURE_EXTRA_FLAGS} --prefix=${SOURCEDIR}/debian/ncbi-blast+ ) 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 - rm -f ${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus/*.a - #mv ${CURDIR}/debian/ncbi-blast-plus/usr/lib/ncbi-blast-plus/*.a ${CURDIR}/debian/ncbi-blast-plus-dev/usr/lib/ncbi-blast-plus/ - #mv ${CURDIR}/debian/ncbi-blast-plus/usr/include ${CURDIR}/debian/ncbi-blast-plus-dev/usr/ - 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+ + rm -f ${CURDIR}/debian/ncbi-blast+/usr/bin/*test* + #mkdir -p ${CURDIR}/debian/ncbi-blast+-dev/usr/lib/ncbi-blast+ + rm -f ${CURDIR}/debian/ncbi-blast+/usr/lib/ncbi-blast+/*.a + #mv ${CURDIR}/debian/ncbi-blast+/usr/lib/ncbi-blast+/*.a ${CURDIR}/debian/ncbi-blast+-dev/usr/lib/ncbi-blast+/ + #mv ${CURDIR}/debian/ncbi-blast+/usr/include ${CURDIR}/debian/ncbi-blast+-dev/usr/ + rm -rf ${CURDIR}/debian/ncbi-blast+/usr/include + find ${CURDIR}/debian/ncbi-blast+/usr/bin/ -type f -not -name "*.p*" | xargs chrpath -d + find ${CURDIR}/debian/ncbi-blast+/usr/lib/ncbi-blast+/*.so | xargs chrpath -d + mv ${CURDIR}/debian/ncbi-blast+/usr/bin/rpsblast ${CURDIR}/debian/ncbi-blast+/usr/bin/rpsblast+ override_dh_clean: dh_clean Modified: trunk/packages/ncbi-blast-plus/trunk/debian/watch =================================================================== --- trunk/packages/ncbi-blast-plus/trunk/debian/watch 2011-05-09 04:56:38 UTC (rev 6794) +++ trunk/packages/ncbi-blast-plus/trunk/debian/watch 2011-05-09 11:48:10 UTC (rev 6795) @@ -1,3 +1,3 @@ version=3 -opts=pasv,filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast-plus/ \ +opts=pasv,filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
