'Add freebayes: Bayesian haplotype-based polymorphism discovery and genotyping'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 20:27:50 2017 -0500
Changeset:	69e8d3d2131d5db04e79604f19c431566d108c9c

Modified Files:
	Makefile
Added Files:
	freebayes/DESCR
	freebayes/Makefile
	freebayes/PLIST
	freebayes/TODO
	freebayes/buildlink3.mk
	freebayes/distinfo

Log Message:
'Add freebayes: 	Bayesian haplotype-based polymorphism discovery and genotyping'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=69e8d3d2131d5db04e79604f19c431566d108c9c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                |  1 +
 freebayes/DESCR         |  1 +
 freebayes/Makefile      | 67 +++++++++++++++++++++++++++++++++++++++++++++++++
 freebayes/PLIST         |  3 +++
 freebayes/TODO          |  1 +
 freebayes/buildlink3.mk | 22 ++++++++++++++++
 freebayes/distinfo      |  6 +++++
 7 files changed, 101 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index ee49f341b7..f4b3fa419b 100644
--- a/Makefile
+++ b/Makefile
@@ -785,6 +785,7 @@ SUBDIR+=	fortunes-it
 SUBDIR+=	foxtrotgps
 SUBDIR+=	fprobe
 SUBDIR+=	fragrouter
+SUBDIR+=	freebayes
 SUBDIR+=	freecad
 SUBDIR+=	freecell
 SUBDIR+=	freedict-tools-xsl
diff --git a/freebayes/DESCR b/freebayes/DESCR
new file mode 100644
index 0000000000..61c7a2badb
--- /dev/null
+++ b/freebayes/DESCR
@@ -0,0 +1 @@
+yesian haplotype-based polymorphism discovery and genotyping.
diff --git a/freebayes/Makefile b/freebayes/Makefile
new file mode 100644
index 0000000000..f061df0b3e
--- /dev/null
+++ b/freebayes/Makefile
@@ -0,0 +1,67 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# # FIXME: Do we need a version >= the submodules bamtools and vcflib?
+# BUILD_DEPENDS=	${LOCALBASE}/include/intervaltree/IntervalTree.h:/usr/wip/math/intervaltree \
+# 		${LOCALBASE}/include/multichoose/multichoose.h:/usr/wip/math/multichoose
+# LIB_DEPENDS=	libbamtools.so:/usr/wip/biology/bamtools \
+# 		libvcflib.so.1:/usr/wip/biology/vcflib \
+# 		libtabix.so.1:/usr/wip/biology/tabixpp \
+# 		libsw.so.1:/usr/wip/biology/smithwaterman \
+# 		libhts.so:/usr/ports/biology/htslib
+# Unknown tool: USE_TOOLS=	compiler:c++11-lang
+# 		-I${LOCALBASE}/include/intervaltree \
+# 		-I${LOCALBASE}/include/vcflib \
+# 		-I${LOCALBASE}/include/multichoose \
+# 		-I${LOCALBASE}/include/smithwaterman
+
+DISTNAME=	freebayes-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG=	${PORTVERSION}
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	https://github.com/ekg/freebayes
+COMMENT=	Bayesian haplotype-based polymorphism discovery and genotyping
+LICENSE=	mit
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_LIBTOOL=	yes
+USE_TOOLS+=	gmake
+
+MAKE_FILE=	Makefile.external-libs
+INSTALL_TARGET=	install-strip
+
+# SUBST_CLASSES+=           compile
+# SUBST_FILES.compile=      ${WRKSRC}/src/Makefile.external-libs
+# SUBST_STAGE.compile=      post-patch
+# SUBST_SED.compile+=       -e "s|-lm|-lm -rpath=${PREFIX}/lib|g"
+
+PORTVERSION=	65c4880d09ec21f7f2755eac9476b607011522f3
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == Linux
+MAKE_FLAGS=	EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
+.else
+MAKE_FLAGS+=	EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
+.endif
+
+.include "../../devel/libexecinfo/buildlink3.mk"
+.include "../../wip/filevercmp/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../wip/intervaltree/buildlink3.mk"
+.include "../../wip/multichoose/buildlink3.mk"
+.include "../../wip/bamtools/buildlink3.mk"
+.include "../../wip/vcflib/buildlink3.mk"
+.include "../../wip/tabixpp/buildlink3.mk"
+.include "../../wip/smithwaterman/buildlink3.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/freebayes/PLIST b/freebayes/PLIST
new file mode 100644
index 0000000000..e9b4294275
--- /dev/null
+++ b/freebayes/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/bamleftalign
+bin/freebayes
diff --git a/freebayes/TODO b/freebayes/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/freebayes/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/freebayes/buildlink3.mk b/freebayes/buildlink3.mk
new file mode 100644
index 0000000000..1972ee53f4
--- /dev/null
+++ b/freebayes/buildlink3.mk
@@ -0,0 +1,22 @@
+# $NetBSD$
+# XXX
+# XXX This file was created automatically using createbuildlink-3.16.
+# XXX After this file has been verified as correct, the comment lines
+# XXX beginning with "XXX" should be removed.  Please do not commit
+# XXX unverified buildlink3.mk files.
+# XXX
+# XXX Packages that only install static libraries or headers should
+# XXX include the following line:
+# XXX
+# XXX	BUILDLINK_DEPMETHOD.freebayes?=	build
+
+BUILDLINK_TREE+=	freebayes
+
+.if !defined(FREEBAYES_BUILDLINK3_MK)
+FREEBAYES_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.freebayes+=	freebayes>=65c4880d09ec21f7f2755eac9476b607011522f3
+BUILDLINK_PKGSRCDIR.freebayes?=	../../wip/freebayes
+.endif	# FREEBAYES_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-freebayes
diff --git a/freebayes/distinfo b/freebayes/distinfo
new file mode 100644
index 0000000000..7de36521ca
--- /dev/null
+++ b/freebayes/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 8e0ba1d24055f949a495f7de017298962367d6ab
+RMD160 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 9b97eede39b7dd9bd9ae513274790567073d2dbb
+SHA512 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 0b401c83a8667fe839d4ef8592b6de35bda33749e1ee448eb9e01613a4854703673c39943c87114ea5450cd46bcb96fa9ebe2f46c5c781149a56c97731680027
+Size (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 2345427 bytes