Attachment 150112 Details for Bug 195591 – Patch to add biology/htslib as a new port.

[patch] Patch to add biology/htslib as a new port.

htslib-1.1.diff (text/plain), 6.04 KB, created by cartwright on 2014-12-02 23:51:14 UTC

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Creator: cartwright

Created: 2014-12-02 23:51:14 UTC

Size: 6.04 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 0)
>+++ Makefile	(working copy)
>@@ -0,0 +1,31 @@
>+# Created by: Reed A. Cartwright <cartwright@asu.edu>
>+# $FreeBSD$
>+
>+PORTNAME=	htslib
>+PORTVERSION=	1.1
>+#PORTREVISION=	0
>+CATEGORIES=	biology devel
>+MASTER_SITES=	GH
>+
>+MAINTAINER=	cartwright@asu.edu
>+COMMENT=	C library for high-throughput sequencing data formats
>+
>+LICENSE=	BSD3CLAUSE MIT
>+LICENSE_COMB=	multi
>+LICENSE_FILE=	${WRKSRC}/LICENSE
>+
>+USE_GITHUB=	yes
>+GH_ACCOUNT=	samtools
>+GH_COMMIT=	a65fba2
>+
>+USES=		gmake
>+USE_LDCONFIG=	yes
>+
>+MAKE_ENV+=	INSTALL_LIB="${INSTALL_LIB}" \
>+		INSTALL_DATA="${INSTALL_DATA}" \
>+		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>+		INSTALL_DIR="${MKDIR}"
>+
>+PLIST_SUB+=	PORTVERSION="${PORTVERSION}"
>+
>+.include <bsd.port.mk>
>
>Property changes on: Makefile
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Added: svn:keywords
>## -0,0 +1 ##
>+FreeBSD=%H
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Index: distinfo
>===================================================================
>--- distinfo	(revision 0)
>+++ distinfo	(working copy)
>@@ -0,0 +1,2 @@
>+SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631
>+SIZE (htslib-1.1.tar.gz) = 957434
>
>Property changes on: distinfo
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 0)
>+++ files/patch-Makefile	(working copy)
>@@ -0,0 +1,64 @@
>+--- Makefile.orig	2014-09-23 14:39:41 UTC
>++++ Makefile
>+@@ -22,33 +22,27 @@
>+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
>+ # DEALINGS IN THE SOFTWARE.
>+ 
>+-CC     = gcc
>+-AR     = ar
>+-RANLIB = ranlib
>++CC    ?= cc
>++AR     = /usr/bin/ar
>++RANLIB = /usr/bin/ranlib
>+ 
>+ # TODO: edit cram code to remove need for -DSAMTOOLS
>+-CPPFLAGS = -I. -DSAMTOOLS=1
>++CPPFLAGS += -I. -DSAMTOOLS=1 -Wno-unused-function -Wno-implicit-function-declaration
>+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
>+-CFLAGS   = -g -Wall -O2
>++CFLAGS   += -g -Wall -O2
>+ EXTRA_CFLAGS_PIC = -fpic
>+-LDFLAGS  =
>+-LDLIBS   =
>++LDFLAGS  +=
>++LDLIBS   +=
>+ 
>+-prefix      = /usr/local
>++prefix      = ${STAGEDIR}${PREFIX}
>+ exec_prefix = $(prefix)
>+ bindir      = $(exec_prefix)/bin
>+ includedir  = $(prefix)/include
>+ libdir      = $(exec_prefix)/lib
>+-mandir      = $(prefix)/share/man
>++mandir      = $(prefix)/man
>+ man1dir     = $(mandir)/man1
>+ man5dir     = $(mandir)/man5
>+-pkgconfigdir= $(libdir)/pkgconfig
>+-
>+-MKDIR_P = mkdir -p
>+-INSTALL = install -p
>+-INSTALL_PROGRAM = $(INSTALL)
>+-INSTALL_DATA    = $(INSTALL) -m 644
>+-INSTALL_DIR     = $(MKDIR_P) -m 755
>++pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
>+ 
>+ BUILT_PROGRAMS = \
>+ 	bgzip \
>+@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \
>+ 	test/test-vcf-api \
>+ 	test/test-vcf-sweep
>+ 
>+-all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
>++all: lib-static lib-shared $(BUILT_PROGRAMS)
>+ 
>+ HTSPREFIX =
>+ include htslib_vars.mk
>+@@ -284,7 +278,7 @@ installdirs:
>+ # and libhts.so.NN (used by client executables at runtime).
>+ 
>+ install-so: libhts.so installdirs
>+-	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
>++	$(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
>+ 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
>+ 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
>+ 
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(revision 0)
>+++ pkg-descr	(working copy)
>@@ -0,0 +1,5 @@
>+HTSlib is an implementation of a unified C library for accessing common file
>+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
>+data. It is the core library used by samtools and bcftools.
>+
>+WWW: http://www.htslib.org/
>
>Property changes on: pkg-descr
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 0)
>+++ pkg-plist	(working copy)
>@@ -0,0 +1,30 @@
>+bin/bgzip
>+bin/tabix
>+include/htslib/bgzf.h
>+include/htslib/faidx.h
>+include/htslib/hfile.h
>+include/htslib/hts.h
>+include/htslib/hts_defs.h
>+include/htslib/kfunc.h
>+include/htslib/khash.h
>+include/htslib/khash_str2int.h
>+include/htslib/klist.h
>+include/htslib/knetfile.h
>+include/htslib/kseq.h
>+include/htslib/ksort.h
>+include/htslib/kstring.h
>+include/htslib/sam.h
>+include/htslib/synced_bcf_reader.h
>+include/htslib/tbx.h
>+include/htslib/vcf.h
>+include/htslib/vcf_sweep.h
>+include/htslib/vcfutils.h
>+lib/libhts.a
>+lib/libhts.so
>+lib/libhts.so.1
>+lib/libhts.so.%%PORTVERSION%%
>+libdata/pkgconfig/htslib.pc
>+man/man1/tabix.1.gz
>+man/man5/faidx.5.gz
>+man/man5/sam.5.gz
>+man/man5/vcf.5.gz
>
>Property changes on: pkg-plist
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property

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Attachments on bug 195591: 150112