Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/bamtools bamtools-2.4.0 as wip /bamtools.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/bamtools bamtools-2.4.0 as wip /bamtools.
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 19:05:46 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 14:05:46 2016 -0500
Changeset:	2b28ae0b313fb4fd8072bf35f0ae9286a7ca8bf2

Added Files:
	bamtools/DESCR
	bamtools/Makefile
	bamtools/PLIST
	bamtools/TODO
	bamtools/buildlink3.mk
	bamtools/distinfo
	bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
	bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/bamtools
bamtools-2.4.0 as wip/bamtools.

"BamTools provides both a programmer's API and an end-user's
toolkit for handling BAM files."

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2b28ae0b313fb4fd8072bf35f0ae9286a7ca8bf2

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

diffstat:
 bamtools/DESCR                                     |  2 +
 bamtools/Makefile                                  | 80 ++++++++++++++++++++++
 bamtools/PLIST                                     | 26 +++++++
 bamtools/TODO                                      |  1 +
 bamtools/buildlink3.mk                             | 12 ++++
 bamtools/distinfo                                  |  8 +++
 .../patch-src_api_internal_io_HostInfo__p.cpp      | 15 ++++
 ...rc_api_internal_io_TcpSocketEngine__unix__p.cpp | 15 ++++
 8 files changed, 159 insertions(+)

diffs:
diff --git a/bamtools/DESCR b/bamtools/DESCR
new file mode 100644
index 0000000..b658e72
--- /dev/null
+++ b/bamtools/DESCR
@@ -0,0 +1,2 @@
+"BamTools provides both a programmer's API and an end-user's
+toolkit for handling BAM files."
diff --git a/bamtools/Makefile b/bamtools/Makefile
new file mode 100644
index 0000000..03ee035
--- /dev/null
+++ b/bamtools/Makefile
@@ -0,0 +1,80 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# # Created by: Dan Siercks
+# # $FreeBSD$
+# Unknown tool: USE_TOOLS=	cmake:outsource
+# USE_LDCONFIG=	yes
+# CMAKE_ARGS+=	-DLIB_DIR=${PREFIX}/lib
+# .include <bsd.port.pre.mk>
+# # Just for speed: Recent compilers have better optimizers
+# Unknown tool: USE_TOOLS=	compiler:c++11-lang
+# .if ${ARCH} == i386
+# MAKE_ENV+=	POPCNT_CAPABILITY=0
+# .endif
+# post-patch:
+# 	${REINPLACE_CMD} -e 's|lib/bamtools|lib|g' \
+# 		work/bamtools-2.4.0/src/api/CMakeLists.txt
+# .include <bsd.port.post.mk>
+
+DISTNAME=	bamtools-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=pezmaster31/}
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	https://github.com/pezmaster31/bamtools
+COMMENT=	API and toolkit for handling BAM files
+# Double-check this
+LICENSE=	mit
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_CMAKE=	yes
+USE_LANGUAGES=	c c++
+CMAKE_ARG_PATH=	..
+CONFIGURE_DIRS=	_build
+
+pre-configure:
+	${MKDIR} ${WRKSRC}/_build
+
+
+WRKSRC=		${WRKDIR}/bamtools-${PORTVERSION}
+
+# Adapt REINPLACE commands to SUBST:
+SUBST_CLASSES+= bamtools_lib
+SUBST_STAGE.bamtools_lib=	post-patch
+SUBST_FILES.bamtools_lib=	${WRKSRC}/src/api/CMakeLists.txt
+SUBST_SED.bamtools_lib=		-e 's|lib/bamtools|lib|g'
+
+#SUBST_CLASSES+=		bluetooth
+#SUBST_STAGE.bluetooth=	post-patch
+#SUBST_FILES.bluetooth=	${WRKSRC}/Commands/Legoctl/Makefile
+#SUBST_SED.bluetooth=	-e 's|-lbluetooth||g'
+
+FETCH_USING=	curl
+
+PORTVERSION=	2.4.0
+#DATADIR=	${PREFIX}/share/bamtools
+#DOCSDIR=	${PREFIX}/share/doc/bamtools
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+# .include "options.mk"
+
+# Specify which directories to create before install.
+# INSTALLATION_DIRS=	bin lib ${PKGMANDIR}/man1 share/doc share/examples
+
+# Linux doesn't have zlib in the base, so just in case...
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bamtools/PLIST b/bamtools/PLIST
new file mode 100644
index 0000000..519b756
--- /dev/null
+++ b/bamtools/PLIST
@@ -0,0 +1,26 @@
+@comment $NetBSD$
+bin/bamtools
+bin/${PKGNAME}
+include/bamtools/api/algorithms/Sort.h
+include/bamtools/api/api_global.h
+include/bamtools/api/BamAlgorithms.h
+include/bamtools/api/BamAlignment.h
+include/bamtools/api/BamAux.h
+include/bamtools/api/BamConstants.h
+include/bamtools/api/BamIndex.h
+include/bamtools/api/BamMultiReader.h
+include/bamtools/api/BamReader.h
+include/bamtools/api/BamWriter.h
+include/bamtools/api/IBamIODevice.h
+include/bamtools/api/SamConstants.h
+include/bamtools/api/SamHeader.h
+include/bamtools/api/SamProgramChain.h
+include/bamtools/api/SamProgram.h
+include/bamtools/api/SamReadGroupDictionary.h
+include/bamtools/api/SamReadGroup.h
+include/bamtools/api/SamSequenceDictionary.h
+include/bamtools/api/SamSequence.h
+include/bamtools/shared/bamtools_global.h
+lib/libbamtools.a
+lib/libbamtools.so
+lib/libbamtools.so.${PKGVERSION}
diff --git a/bamtools/TODO b/bamtools/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/bamtools/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/bamtools/buildlink3.mk b/bamtools/buildlink3.mk
new file mode 100644
index 0000000..673e18f
--- /dev/null
+++ b/bamtools/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	bamtools
+
+.if !defined(BAMTOOLS_BUILDLINK3_MK)
+BAMTOOLS_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.bamtools+=	bamtools>=2.4.0
+BUILDLINK_PKGSRCDIR.bamtools?=	../../wip/bamtools
+.endif	# BAMTOOLS_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-bamtools
diff --git a/bamtools/distinfo b/bamtools/distinfo
new file mode 100644
index 0000000..4e9fb8b
--- /dev/null
+++ b/bamtools/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (bamtools-2.4.0.tar.gz) = 7b98d88a12c022bbcabdbd7c0e92c5d2bc4a3f6b
+RMD160 (bamtools-2.4.0.tar.gz) = e2269a9d1af2ebf1a38f2fd5f4d75f3f2426b358
+SHA512 (bamtools-2.4.0.tar.gz) = 33332f290e72ed3943c9df6022a44cfcd358ae1c1d41b1b494c7087a66e865529721ee6230212313d482cb66764573e300f362fee9ccbf3c0da18544bf2e9425
+Size (bamtools-2.4.0.tar.gz) = 539779 bytes
+SHA1 (patch-src_api_internal_io_HostInfo__p.cpp) = 041bdbccd9b5906b5c3d6ba3c285d674ccd4f509
+SHA1 (patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp) = 81ba4f71f85724ddc38039fc621076b1570eaf02
diff --git a/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp b/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
new file mode 100644
index 0000000..95e3e69
--- /dev/null
+++ b/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Needed for type definitions on FreeBSD
+
+--- src/api/internal/io/HostInfo_p.cpp.orig	2015-06-16 16:50:53 UTC
++++ src/api/internal/io/HostInfo_p.cpp
+@@ -11,6 +11,8 @@
+ using namespace BamTools;
+ using namespace BamTools::Internal;
+ 
++#include <netinet/in.h>
++
+ // platorm-specifics
+ #ifdef _WIN32
+ #  include "api/internal/io/NetWin_p.h"
diff --git a/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
new file mode 100644
index 0000000..9f2e426
--- /dev/null
+++ b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Needed for type definitions on FreeBSD
+
+--- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2015-06-16 16:50:53 UTC
++++ src/api/internal/io/TcpSocketEngine_unix_p.cpp
+@@ -12,6 +12,8 @@
+ using namespace BamTools;
+ using namespace BamTools::Internal;
+ 
++#include <netinet/in.h>
++
+ #ifdef SUN_OS
+ #include <sys/filio.h> 
+ #endif
Prev by Date: Add new package seqtk to Makefile
Next by Date: Add new package bamtools to Makefile
Previous by Thread: Add new package seqtk to Makefile
Next by Thread: Add new package bamtools to Makefile
Indexes:
Home | Main Index | Thread Index | Old Index