'Add unanimity: Consensus library and applications'

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sat Sep 17 09:14:48 2016 -0500
Changeset:	7def4ead6dec3ae35e6bb55739a4d0e4258eb411

Modified Files:
	Makefile
Added Files:
	unanimity/DESCR
	unanimity/Makefile
	unanimity/PLIST
	unanimity/TODO
	unanimity/distinfo
	unanimity/patches/patch-cmake_uny-gitsha1.cmake

Log Message:
'Add unanimity: 	Consensus library and applications'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7def4ead6dec3ae35e6bb55739a4d0e4258eb411

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

diffstat:
 Makefile                                        |  1 +
 unanimity/DESCR                                 |  1 +
 unanimity/Makefile                              | 52 +++++++++++++++++++++++++
 unanimity/PLIST                                 |  2 +
 unanimity/TODO                                  |  1 +
 unanimity/distinfo                              |  7 ++++
 unanimity/patches/patch-cmake_uny-gitsha1.cmake | 15 +++++++
 7 files changed, 79 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index cb8685f..1abb294 100644
--- a/Makefile
+++ b/Makefile
@@ -4189,6 +4189,7 @@ SUBDIR+=	ukncbtl
 SUBDIR+=	umix
 SUBDIR+=	umurmur
 SUBDIR+=	unagi
+SUBDIR+=	unanimity
 SUBDIR+=	unarchiver-clt
 SUBDIR+=	undo-tree
 SUBDIR+=	unicorn5hc
diff --git a/unanimity/DESCR b/unanimity/DESCR
new file mode 100644
index 0000000..bcd2f88
--- /dev/null
+++ b/unanimity/DESCR
@@ -0,0 +1 @@
+Pacific Biosciences Consensus library and applications.
diff --git a/unanimity/Makefile b/unanimity/Makefile
new file mode 100644
index 0000000..14da5df
--- /dev/null
+++ b/unanimity/Makefile
@@ -0,0 +1,52 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Tue Sep 13 12:49:29 CDT 2016               #
+###########################################################
+
+# FIXME: Searches /usr/local/include before /usr/local/include/PacBio
+# so it will pick up the wrong seqan headers if biology/seqan is installed.
+# Hopefully PacBio's seqan patches will be in the next seqan release.
+
+DISTNAME=	unanimity-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=PacificBiosciences/}
+GITHUB_PROJECT=	unanimity
+GITHUB_TAG=	054c59530f7ee7c3ce0adde4524f367e8d0244cd
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://github.com/PacificBiosciences/unanimity
+COMMENT=	Consensus library and applications
+LICENSE=	modified-bsd
+
+MAKE_JOBS_SAFE=	yes
+
+USE_LANGUAGES=	c c++
+USE_CMAKE=	yes
+GCC_REQD=	4.9
+CMAKE_ARGS=	-DHTSLIB_INCLUDE_DIRS:STRING=${PREFIX}/include/htslib \
+		-DHTSLIB_LIBRARIES:STRING="-L${PREFIX}/lib -lhts" \
+		-DPacBioBAM_INCLUDE_DIRS:STRING=${PREFIX}/include/pbbam \
+		-DPacBioBAM_LIBRARIES:STRING="-L${PREFIX}/lib -lpbbam" \
+		-DSEQAN_INCLUDE_DIRS:STRING=${PREFIX}/include/PacBio \
+		-Dpbcopper_INCLUDE_DIRS=${PREFIX}/include \
+		-Dpbcopper_LIBRARIES="-L${PREFIX}/lib -lpbcopper"
+
+CXXFLAGS+=	-O2
+
+# Why is this needed with openssl/buildlink3.mk?
+LDFLAGS+=	-lssl
+
+WRKSRC=		${WRKDIR}/unanimity-${GITHUB_TAG}
+
+PORTVERSION=	2016.09.13
+
+.include "../../wip/pbseqan/buildlink3.mk"
+.include "../../wip/pbbam/buildlink3.mk"
+.include "../../wip/pbcopper/buildlink3.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../security/openssl/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/unanimity/PLIST b/unanimity/PLIST
new file mode 100644
index 0000000..e486b5d
--- /dev/null
+++ b/unanimity/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/ccs
diff --git a/unanimity/TODO b/unanimity/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/unanimity/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/unanimity/distinfo b/unanimity/distinfo
new file mode 100644
index 0000000..3765d08
--- /dev/null
+++ b/unanimity/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = 106252368e049e716426fdae771db82cb79f13a9
+RMD160 (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = eebee01595e399d80967923d3533f126e7e9a512
+SHA512 (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = af65bc699af545141496e996900d7fae8a65b1060907fc0c1070109c46eca2fbf787ea085905e7344ebf0f2a3fde7de9901a8dd0796eb3ecd01f03e06c8b15f9
+Size (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = 5423410 bytes
+SHA1 (patch-cmake_uny-gitsha1.cmake) = 0323b8dda91693bd02af715efe9b4f6bc2837263
diff --git a/unanimity/patches/patch-cmake_uny-gitsha1.cmake b/unanimity/patches/patch-cmake_uny-gitsha1.cmake
new file mode 100644
index 0000000..e915360
--- /dev/null
+++ b/unanimity/patches/patch-cmake_uny-gitsha1.cmake
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Not using git to fetch.
+
+--- cmake/uny-gitsha1.cmake.orig	2016-08-12 12:47:37 UTC
++++ cmake/uny-gitsha1.cmake
+@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
+ function(find_git_sha1 _GIT_SHA1)
+     find_package(Git QUIET REQUIRED)
+     execute_process(COMMAND
+-        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
++        echo 054c595
+         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+         RESULT_VARIABLE res
+         OUTPUT_VARIABLE out