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biology/ncbi-blast+: Upgrade to 2.7.1
Patch Makefile.in.top to cleanly support DESTDIR Also resolves 225002, conflict with libproj PR: 226037 Reported by: wen Reviewed by: mat rene Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14854
This commit is contained in:
Jason W. Bacon
parent
099e97d4b1
commit
9053d41234
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=465726
@ -1,12 +1,10 @@
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# $FreeBSD$
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PORTNAME= blast+
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PORTVERSION= 2.5.0
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PORTREVISION= 3
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CATEGORIES= biology
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MASTER_SITES= http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \
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http://acadix.biz/Ports/distfiles/
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PKGNAMEPREFIX= ncbi-
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PORTNAME= ncbi-blast+
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DISTVERSION= 2.7.1
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CATEGORIES= biology perl5 python
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MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
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https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
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DISTNAME= ncbi-blast-${PORTVERSION}+-src
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MAINTAINER= jwb@FreeBSD.org
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@ -15,43 +13,55 @@ COMMENT= NCBI implementation of Basic Local Alignment Search Tool
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LICENSE= PD
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LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE
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LIB_DEPENDS= libpcre.so:devel/pcre
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LIB_DEPENDS= libpcre.so:devel/pcre \
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liblmdb.so:databases/lmdb \
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liblzo2.so:archivers/lzo2 \
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libgnutls.so:security/gnutls \
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libtspi.so:security/trousers \
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libgmp.so:math/gmp \
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libidn2.so:dns/libidn2 \
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libnettle.so:security/nettle \
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libhogweed.so:security/nettle \
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libtasn1.so:security/libtasn1 \
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libp11-kit.so:security/p11-kit \
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libgcrypt.so:security/libgcrypt \
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libgpg-error.so:security/libgpg-error \
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libsqlite3.so:databases/sqlite3
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RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils
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WRKSRC= ${WRKDIR}/${DISTNAME}/c++
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GNU_CONFIGURE= yes
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USES= gmake shebangfix perl5 python
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USES= compiler:openmp gmake shebangfix perl5 python
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SHEBANG_FILES= src/app/blast/legacy_blast.pl \
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src/app/blast/update_blastdb.pl \
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src/app/winmasker/windowmasker_2.2.22_adapter.py
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MAKE_JOBS_UNSAFE= yes
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# Requires openmp
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USE_GCC= yes
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USE_LDCONFIG= yes
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GNU_CONFIGURE= yes
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# The test for amq can hang, but amq is not needed so just avoid the test
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CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
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# configure chooses /usr/local/bin/ar with no flags
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# FreeBSD boost port flagged by configure as untested version
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CONFIGURE_ARGS+=AR="ar cr" --without-boost
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# --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do
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# a postinstall mv.
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CONFIGURE_ARGS+= AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++
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WRKSRC_SUBDIR= c++
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MAKE_JOBS_UNSAFE= yes
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# Fix "undefined _ThreadRuneLocale" error on 10.0
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# Fix unknown options in configure
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# Add staging support to configure-generated Makefile
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post-patch:
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${REINPLACE_CMD} \
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@${REINPLACE_CMD} \
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-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \
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-e '/--infodir=DIR/d' \
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-e '/--mandir=DIR/d' \
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${WRKSRC}/src/build-system/configure
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${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \
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${WRKSRC}/src/build-system/Makefile.in.top
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post-install:
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${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so
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@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
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@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
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@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
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${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so
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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1480648908
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SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54
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SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544
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TIMESTAMP = 1518995346
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SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca
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SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824
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@ -1,11 +1,32 @@
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--- src/build-system/Makefile.in.top.orig 2014-11-13 01:41:55.000000000 +0900
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+++ src/build-system/Makefile.in.top 2016-12-02 16:39:58.415910000 +0900
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@@ -51,7 +51,7 @@
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--- src/build-system/Makefile.in.top.orig 2018-03-27 03:40:40 UTC
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+++ src/build-system/Makefile.in.top
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@@ -37,21 +37,21 @@ check: $(PROJECTS)
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fi
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install-toolkit:
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- -$(RMDIR) $(pincludedir)
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- $(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
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- $(INSTALL) $(lbindir)/* $(bindir)
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- $(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
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+ -$(RMDIR) $(DESTDIR)$(pincludedir)
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+ $(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir)
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+ $(INSTALL) $(lbindir)/* $(DESTDIR)$(bindir)
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+ $(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir)
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if test -d $(llibdir)/ncbi; then \
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- cp -pPR $(llibdir)/ncbi $(libdir)/; \
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+ cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \
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fi
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- -rm -f $(libdir)/lib*-static.a
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- cd $(libdir) && \
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+ -rm -f $(DESTDIR)$(libdir)/lib*-static.a
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+ cd $(DESTDIR)$(libdir) && \
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for x in *.a; do \
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$(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
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done
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cd $(includedir0) && find * -name CVS -prune -o -print |\
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cpio -pd $(pincludedir)
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- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
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+ cd $(incdir) && find * | cpio -pd $(pincludedir)
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for d in $(includedir0) $(incdir); do \
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cd $$d && find * -name .svn -prune -o -print | \
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- cpio -pd $(pincludedir) ; \
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+ cpio -pd $(DESTDIR)$(pincludedir) ; \
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done
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## set up appropriate build and status directories somewhere under $(libdir)?
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install-gbench:
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@ -1,11 +1,30 @@
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--- src/build-system/configure.orig 2016-09-09 21:04:16.000000000 +0900
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+++ src/build-system/configure 2016-12-02 15:04:04.258800000 +0900
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@@ -1715,7 +1715,7 @@
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| --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
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| --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
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--- src/build-system/configure.orig 2017-10-18 15:21:39 UTC
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+++ src/build-system/configure
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@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
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| --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
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| --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
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| --datadir=* | --sysconfdir=* | --localstatedir=* \
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- | --with-runpath=* | --with-relative-runpath=* \
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+ | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
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| --with-experimental=* | --with-extra-action=* | --with-build-root=* \
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| --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
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| --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
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@@ -1828,9 +1828,7 @@ Fine tuning of the installation director
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--oldincludedir=DIR C header files for non-gcc [/usr/include]
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--datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
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--datadir=DIR read-only architecture-independent data [DATAROOTDIR]
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- --infodir=DIR info documentation [DATAROOTDIR/info]
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--localedir=DIR locale-dependent data [DATAROOTDIR/locale]
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- --mandir=DIR man documentation [DATAROOTDIR/man]
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--docdir=DIR documentation root [DATAROOTDIR/doc/ncbi-tools--]
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--htmldir=DIR html documentation [DOCDIR]
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--dvidir=DIR dvi documentation [DOCDIR]
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@@ -8086,7 +8084,7 @@ case "$host_os:$compiler" in
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esac
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if test "$with_mt" != "no" ; then
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- CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE"
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+ CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL"
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LIBS="$LIBS $THREAD_LIBS"
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case "$host_os:$compiler" in
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solaris2.??:* | solaris*:GCC | *:Compaq | irix* | aix* | darwin* | cygwin*)
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@ -1,8 +1,7 @@
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The Basic Local Alignment Search Tool (BLAST) finds regions of local
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similarity between sequences. The program compares nucleotide or protein
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sequences to sequence databases and calculates the statistical
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significance of matches. BLAST can be used to infer functional and
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evolutionary relationships between sequences as well as help identify
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members of gene families.
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The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
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between sequences. The program compares nucleotide or protein sequences to
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sequence databases and calculates the statistical significance of matches.
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BLAST can be used to infer functional and evolutionary relationships between
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sequences as well as help identify members of gene families.
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WWW: http://blast.ncbi.nlm.nih.gov
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