'Add freebayes: Bayesian haplotype-based polymorphism discovery and genotyping'
This commit is contained in:
Jason Bacon
parent
8528abeec1
commit
69e8d3d213
1
Makefile
1
Makefile
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@ -785,6 +785,7 @@ SUBDIR+= fortunes-it
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SUBDIR+= foxtrotgps
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SUBDIR+= fprobe
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SUBDIR+= fragrouter
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SUBDIR+= freebayes
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SUBDIR+= freecad
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SUBDIR+= freecell
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SUBDIR+= freedict-tools-xsl
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1
freebayes/DESCR
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1
freebayes/DESCR
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@ -0,0 +1 @@
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yesian haplotype-based polymorphism discovery and genotyping.
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67
freebayes/Makefile
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67
freebayes/Makefile
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@ -0,0 +1,67 @@
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# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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###########################################################
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# Unconverted and partially converted FreeBSD port syntax:
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# # FIXME: Do we need a version >= the submodules bamtools and vcflib?
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# BUILD_DEPENDS= ${LOCALBASE}/include/intervaltree/IntervalTree.h:/usr/wip/math/intervaltree \
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# ${LOCALBASE}/include/multichoose/multichoose.h:/usr/wip/math/multichoose
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# LIB_DEPENDS= libbamtools.so:/usr/wip/biology/bamtools \
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# libvcflib.so.1:/usr/wip/biology/vcflib \
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# libtabix.so.1:/usr/wip/biology/tabixpp \
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# libsw.so.1:/usr/wip/biology/smithwaterman \
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# libhts.so:/usr/ports/biology/htslib
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# Unknown tool: USE_TOOLS= compiler:c++11-lang
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# -I${LOCALBASE}/include/intervaltree \
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# -I${LOCALBASE}/include/vcflib \
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# -I${LOCALBASE}/include/multichoose \
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# -I${LOCALBASE}/include/smithwaterman
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DISTNAME= freebayes-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
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GITHUB_TAG= ${PORTVERSION}
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MAINTAINER= dsiercks@uwm.edu
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HOMEPAGE= https://github.com/ekg/freebayes
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COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
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LICENSE= mit
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# Just assuming C and C++: Adjust this!
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USE_LANGUAGES= c c++
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USE_LIBTOOL= yes
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USE_TOOLS+= gmake
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MAKE_FILE= Makefile.external-libs
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INSTALL_TARGET= install-strip
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# SUBST_CLASSES+= compile
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# SUBST_FILES.compile= ${WRKSRC}/src/Makefile.external-libs
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# SUBST_STAGE.compile= post-patch
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# SUBST_SED.compile+= -e "s|-lm|-lm -rpath=${PREFIX}/lib|g"
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PORTVERSION= 65c4880d09ec21f7f2755eac9476b607011522f3
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.include "../../mk/bsd.prefs.mk"
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.if ${OPSYS} == Linux
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MAKE_FLAGS= EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
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.else
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MAKE_FLAGS+= EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
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.endif
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.include "../../devel/libexecinfo/buildlink3.mk"
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.include "../../wip/filevercmp/buildlink3.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../wip/intervaltree/buildlink3.mk"
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.include "../../wip/multichoose/buildlink3.mk"
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.include "../../wip/bamtools/buildlink3.mk"
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.include "../../wip/vcflib/buildlink3.mk"
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.include "../../wip/tabixpp/buildlink3.mk"
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.include "../../wip/smithwaterman/buildlink3.mk"
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.include "../../wip/htslib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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3
freebayes/PLIST
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3
freebayes/PLIST
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@ -0,0 +1,3 @@
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@comment $NetBSD$
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bin/bamleftalign
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bin/freebayes
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1
freebayes/TODO
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1
freebayes/TODO
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@ -0,0 +1 @@
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Clean up and test
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22
freebayes/buildlink3.mk
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22
freebayes/buildlink3.mk
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@ -0,0 +1,22 @@
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# $NetBSD$
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# XXX
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# XXX This file was created automatically using createbuildlink-3.16.
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# XXX After this file has been verified as correct, the comment lines
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# XXX beginning with "XXX" should be removed. Please do not commit
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# XXX unverified buildlink3.mk files.
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# XXX
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# XXX Packages that only install static libraries or headers should
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# XXX include the following line:
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# XXX
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# XXX BUILDLINK_DEPMETHOD.freebayes?= build
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BUILDLINK_TREE+= freebayes
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.if !defined(FREEBAYES_BUILDLINK3_MK)
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FREEBAYES_BUILDLINK3_MK:=
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BUILDLINK_API_DEPENDS.freebayes+= freebayes>=65c4880d09ec21f7f2755eac9476b607011522f3
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BUILDLINK_PKGSRCDIR.freebayes?= ../../wip/freebayes
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.endif # FREEBAYES_BUILDLINK3_MK
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BUILDLINK_TREE+= -freebayes
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6
freebayes/distinfo
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6
freebayes/distinfo
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@ -0,0 +1,6 @@
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$NetBSD$
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SHA1 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 8e0ba1d24055f949a495f7de017298962367d6ab
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RMD160 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 9b97eede39b7dd9bd9ae513274790567073d2dbb
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SHA512 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 0b401c83a8667fe839d4ef8592b6de35bda33749e1ee448eb9e01613a4854703673c39943c87114ea5450cd46bcb96fa9ebe2f46c5c781149a56c97731680027
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Size (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 2345427 bytes
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