'Add daligner: Find all significant local alignments between reads'
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1
Makefile
1
Makefile
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@ -458,6 +458,7 @@ SUBDIR+= d-feet
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SUBDIR+= d1x-rebirth
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SUBDIR+= d2x-rebirth
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SUBDIR+= d4x
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SUBDIR+= daligner
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SUBDIR+= daphne
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SUBDIR+= daq
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SUBDIR+= darcnes-svgalib
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@ -0,0 +1,3 @@
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Find all significant local alignments between reads.
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WWW: https://github.com/thegenemyers/DALIGNER
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@ -0,0 +1,74 @@
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# $NetBSD$
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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## Must use the same version of dazz_db, daligner, pypeflow, and falcon!
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DISTNAME= daligner-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= http://acadix.biz/Ports/distfiles/
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EXTRACT_SUFX= .tar.xz
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MAINTAINER= bacon4000@gmail.com
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COMMENT= Find all significant local alignments between reads
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# Double-check this
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LICENSE= modified-bsd
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# Pessimistic assumption. Test and change if possible.
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# MAKE_JOBS_SAFE= no
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# Just assuming C and C++: Adjust this!
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USE_LANGUAGES= c
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USE_TOOLS+= gmake
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# OS X Snow Leopard doesn't suppot no-unused-result and dies of an
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# internal compiler error if we use -O2 or higher
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SUBST_CLASSES+= makefile
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SUBST_STAGE.makefile= post-patch
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SUBST_FILES.makefile= ${WRKSRC}/GNUmakefile
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SUBST_SED.makefile= -e 's|-Wno-unused-result||g'
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SUBST_SED.makefile+= -e 's|-O3|-O|g'
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CFLAGS+= -I${PREFIX}/include
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MAKE_FILE= GNUmakefile
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PORTVERSION= 2015.10.28
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AUTO_MKDIRS= yes
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post-patch:
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for f in ${WRKSRC}/py_utils/*.py; do \
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${PRINTF} "#!${PYTHONBIN}\\n" > $$f.temp; \
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${CAT} $$f >> $$f.temp; \
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${MV} -f $$f.temp $$f; \
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done
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do-install:
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${INSTALL_PROGRAM} \
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${WRKSRC}/DB2Falcon \
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${WRKSRC}/HPCdaligner \
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${WRKSRC}/HPCmapper \
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${WRKSRC}/LA4Falcon \
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${WRKSRC}/LAcat \
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${WRKSRC}/LAcheck \
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${WRKSRC}/LAmerge \
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${WRKSRC}/LAshow \
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${WRKSRC}/LAsort \
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${WRKSRC}/LAsplit \
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${WRKSRC}/daligner \
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${WRKSRC}/daligner_p \
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${DESTDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} \
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${WRKSRC}/py_utils/*.py \
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${DESTDIR}${PREFIX}/bin
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${INSTALL_DATA} \
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${WRKSRC}/*.h \
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${DESTDIR}${PREFIX}/include
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${AR} rs ${DESTDIR}${PREFIX}/lib/libdaligner.a \
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${WRKSRC}/align.o
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.include "../../wip/dazz_db/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,21 @@
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@comment $NetBSD$
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bin/daligner
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bin/daligner_p
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bin/DAPipe.py
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bin/DAPI.py
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bin/DB2Falcon
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bin/DBLA_to_falcon.py
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bin/HPCdaligner
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bin/HPCmapper
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bin/LA4Falcon
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bin/LAcat
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bin/LAcheck
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bin/LAmerge
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bin/LAPipe.py
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bin/LAPI.py
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bin/LAshow
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bin/LAsort
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bin/LAsplit
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include/align.h
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include/filter.h
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lib/libdaligner.a
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@ -0,0 +1 @@
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Clean up and test
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@ -0,0 +1,12 @@
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# $NetBSD$
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BUILDLINK_TREE+= daligner
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.if !defined(DALIGNER_BUILDLINK3_MK)
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DALIGNER_BUILDLINK3_MK:=
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BUILDLINK_API_DEPENDS.daligner+= daligner-2015.10.28{,nb*}
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BUILDLINK_PKGSRCDIR.daligner?= ../../wip/daligner
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.endif # DALIGNER_BUILDLINK3_MK
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BUILDLINK_TREE+= -daligner
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@ -0,0 +1,6 @@
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$NetBSD$
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SHA1 (daligner-2015.10.28.tar.xz) = b11d0e62f2e14a2bf10c51d2118fc9b1ae5925ea
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RMD160 (daligner-2015.10.28.tar.xz) = 813725f49fb82431b7c0397874732bc5368c84c6
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SHA512 (daligner-2015.10.28.tar.xz) = 39e3e760b378711df043223805670ee256ac7f0a8c29d74bc103ffd09844fa09fdfb02925c76ce841fa5c3b51f53f385f3edb66fafed824411f7cc60f3655579
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Size (daligner-2015.10.28.tar.xz) = 57128 bytes
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