sci-biology/samtools: Version BUmp, #485450

(Portage version: 2.2.6/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 251 insertions, 1 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 444e7cb5b803..4a89c3eb995a 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/samtools
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.12 2013/03/29 17:29:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.13 2013/09/20 17:15:46 jlec Exp $
+
+*samtools-0.1.19 (20 Sep 2013)
+
+  20 Sep 2013; Justin Lecher <jlec@gentoo.org> +samtools-0.1.19.ebuild,
+  +files/samtools-0.1.19-buildsystem.patch:
+  Version BUmp, #485450
 
 *samtools-0.1.18-r3 (29 Mar 2013)
 
diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
new file mode 100644
index 000000000000..2abffccb2015
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
@@ -0,0 +1,183 @@
+ Makefile          | 22 +++++++++++-----------
+ bcftools/Makefile | 12 ++++++------
+ misc/Makefile     | 28 ++++++++++++++--------------
+ 3 files changed, 31 insertions(+), 31 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 2f51bfc..4dda5a4 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2
+-#LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
+-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
++CC?=			gcc
++CFLAGS?=		-g -Wall -O2
++#LDFLAGS+=		-Wl,-rpath,\$$ORIGIN/../lib
++CPPFLAGS+=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
+ KNETFILE_O=	knetfile.o
+ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+ 			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+@@ -21,14 +21,14 @@ LIBCURSES=	-lcurses # -lXCurses
+ .PHONY: all lib
+ 
+ .c.o:
+-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+ 
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ 		@target=`echo $@ | sed s/-recur//`; \
+ 		wdir=`pwd`; \
+ 		list='$(SUBDIRS)'; for subdir in $$list; do \
+ 			cd $$subdir; \
+-			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ 				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ 			cd $$wdir; \
+ 		done;
+@@ -44,16 +44,16 @@ libbam.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
+ 
+ samtools:lib-recur $(AOBJS)
+-		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
+ 
+ razip:razip.o razf.o $(KNETFILE_O)
+-		$(CC) $(CFLAGS) -o $@ $^ -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz
+ 
+ bgzip:bgzip.o bgzf.o $(KNETFILE_O)
+-		$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread
+ 
+ bgzf.o:bgzf.c bgzf.h
+-		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
+ 
+ razip.o:razf.h
+ bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
+@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS)
+ 		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
+ 
+ libbam.so.1-local:$(LOBJS)
+-		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
++		$(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
+ 
+ dylib:
+ 		@$(MAKE) cleanlocal; \
+diff --git a/bcftools/Makefile b/bcftools/Makefile
+index be831de..7ef796c 100644
+--- a/bcftools/Makefile
++++ b/bcftools/Makefile
+@@ -1,6 +1,6 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
++CC?=			gcc
++CFLAGS?=		-g -Wall -O2 #-m64 #-arch ppc
++CPPFLAGS+=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS=		bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+ OMISC=		..
+ AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
+@@ -11,14 +11,14 @@ SUBDIRS=	.
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+-		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
+ 
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ 		@target=`echo $@ | sed s/-recur//`; \
+ 		wdir=`pwd`; \
+ 		list='$(SUBDIRS)'; for subdir in $$list; do \
+ 			cd $$subdir; \
+-			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ 				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ 			cd $$wdir; \
+ 		done;
+@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
+ 
+ bcftools:lib $(AOBJS)
+-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
+ 
+ bcf.o:bcf.h
+ vcf.o:bcf.h
+diff --git a/misc/Makefile b/misc/Makefile
+index d36e7ac..7ae1dc3 100644
+--- a/misc/Makefile
++++ b/misc/Makefile
+@@ -1,8 +1,8 @@
+-CC=			gcc
+-CXX=		g++
+-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+-CXXFLAGS=	$(CFLAGS)
+-DFLAGS=		-D_FILE_OFFSET_BITS=64
++CC?=			gcc
++CXX?=		g++
++CFLAGS?=		-g -Wall -O2 #-m64 #-arch ppc
++CXXFLAGS?=	$(CFLAGS)
++CPPFLAGS+=		-D_FILE_OFFSET_BITS=64
+ OBJS=		
+ PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
+ INCLUDES=	-I..
+@@ -11,7 +11,7 @@ SUBDIRS=	.
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+ 
+ all:$(PROG)
+ 
+@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+ 		wdir=`pwd`; \
+ 		list='$(SUBDIRS)'; for subdir in $$list; do \
+ 			cd $$subdir; \
+-			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ 				INCLUDES="$(INCLUDES)" $$target || exit 1; \
+ 			cd $$wdir; \
+ 		done;
+@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+ lib:
+ 
+ bamcheck:bamcheck.o
+-		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
+ 
+ bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+ 		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
+ 
+ ace2sam:ace2sam.o
+-		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz
+ 
+ wgsim:wgsim.o
+-		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz
+ 
+ md5fa:md5.o md5fa.o md5.h ../kseq.h
+-		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz
+ 
+ md5sum-lite:md5sum-lite.o
+-		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o
+ 
+ md5sum-lite.o:md5.c md5.h
+ 		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+ 
+ maq2sam-short:maq2sam.c
+-		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz
+ 
+ maq2sam-long:maq2sam.c
+-		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
++		$(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz
+ 
+ md5fa.o:md5.h md5fa.c
+ 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
diff --git a/sci-biology/samtools/samtools-0.1.19.ebuild b/sci-biology/samtools/samtools-0.1.19.ebuild
new file mode 100644
index 000000000000..ee4cb51fdf52
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.19.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19.ebuild,v 1.1 2013/09/20 17:15:46 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://samtools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="sys-libs/ncurses"
+RDEPEND="${CDEPEND}
+	dev-lang/lua
+	dev-lang/perl"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+	tc-export CC AR
+}
+
+src_compile() {
+	local _ncurses="$(pkg-config --libs ncurses)"
+	emake dylib LIBCURSES="${_ncurses}"
+	emake LIBCURSES="${_ncurses}"
+}
+
+src_install() {
+	dobin samtools $(find bcftools misc -type f -executable)
+
+	python_replicate_script "${ED}"/usr/bin/varfilter.py
+
+	dolib.so libbam.so.1
+	dosym libbam.so.1 /usr/$(get_libdir)/libbam.so
+
+	insinto /usr/include/bam
+	doins *.h
+
+	doman ${PN}.1
+	dodoc AUTHORS NEWS
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples
+	fi
+}