sci-biology/samtools: Version BUmp

(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 244 insertions, 2 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 41e7af409c0d..1813f4f41444 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/samtools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.20 2014/09/25 15:20:53 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.21 2015/01/06 12:57:48 jlec Exp $
+
+*samtools-1.1 (06 Jan 2015)
+
+  06 Jan 2015; Justin Lecher <jlec@gentoo.org> +samtools-1.1.ebuild,
+  +files/samtools-1.1-buildsystem.patch:
+  Version BUmp
 
 *samtools-1.0-r1 (25 Sep 2014)
 
diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
new file mode 100644
index 000000000000..b9ae77de67d2
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
@@ -0,0 +1,153 @@
+ Makefile | 76 ++++++++++++++++++++++++++++++++++++----------------------------
+ 1 file changed, 43 insertions(+), 33 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 43cefc3..743dd07 100644
+--- a/Makefile
++++ b/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-CPPFLAGS = $(DFLAGS) $(INCLUDES)
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
+-LDLIBS   =
++CC       ?= gcc
++CPPFLAGS += $(DFLAGS) $(INCLUDES)
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  +=
++LDLIBS   +=
++BAMLIB   ?= libbam.a
+ DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+             sam_header.o bam_plbuf.o
+@@ -42,6 +43,7 @@ LIBCURSES=  -lcurses # -lXCurses
+ prefix      = /usr/local
+ exec_prefix = $(prefix)
+ bindir      = $(exec_prefix)/bin
++libdir      = $(exec_prefix)/lib
+ mandir      = $(prefix)/share/man
+ man1dir     = $(mandir)/man1
+ 
+@@ -115,63 +117,71 @@ version.h:
+ .c.o:
+ 	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+ 
++$(LOBJS):
++	$(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+ 
+-lib:libbam.a
++
++lib:libbam.a libbam.so.1.0
+ 
+ libbam.a:$(LOBJS)
+ 	$(AR) -csru $@ $(LOBJS)
+ 
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+-	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
++libbam.so.1.0:$(LOBJS)
++	$(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++	ln -sf $@ libbam.so.0
++	ln -sf $@ libbam.so
++
++samtools: $(AOBJS) lib
++	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+ 
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h)
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h)
+ sam_h = sam.h $(htslib_sam_h) $(bam_h)
+-sample_h = sample.h $(HTSDIR)/htslib/kstring.h
++sample_h = sample.h
+ 
+ bam.o: bam.c $(bam_h) sam_header.h
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h
++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
+ bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h
+ bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
+ bam_aux.o: bam_aux.c
+ bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
+ bam_color.o: bam_color.c $(bam_h)
+-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
+-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
+-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h
++bam_import.o: bam_import.c $(bam_h)
++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h)
++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h)
+ bam_mate.o: bam_mate.c $(bam_h)
+ bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h
+ bam_pileup.o: bam_pileup.c $(sam_h)
+ bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
+-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
+ bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
+-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
+-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
+-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h)
++bam_rmdup.o: bam_rmdup.c $(sam_h)
++bam_rmdupse.o: bam_rmdupse.c $(sam_h)
++bam_sort.o: bam_sort.c  $(htslib_sam_h)
+ bam_stat.o: bam_stat.c $(bam_h) samtools.h
+ bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
+ bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
+ bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
+ bam_flags.o: bam_flags.c $(sam_h)
+-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
++bamshuf.o: bamshuf.c $(htslib_sam_h)  samtools.h
+ bamtk.o: bamtk.c $(bam_h) version.h samtools.h
+-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
+-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
++bedcov.o: bedcov.c $(htslib_sam_h)
++bedidx.o: bedidx.c
+ cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
+-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
++errmod.o: errmod.c errmod.h
+ kaln.o: kaln.c kaln.h
+ kprobaln.o: kprobaln.c kprobaln.h
+ padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
+-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
++phase.o: phase.c $(htslib_sam_h) errmod.h
+ sam.o: sam.c $(htslib_faidx_h) $(sam_h)
+-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h
+-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
+-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
+-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
+-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)
++sam_header.o: sam_header.c sam_header.h
++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h
++sample.o: sample.c $(sample_h)
++stats_isize.o: stats_isize.c stats_isize.h
++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h)
+ 
+ 
+ # test programs
+@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib
+ # For tests that might use it, set $REF_PATH explicitly to use only reference
+ # areas within the test suite (or set it to ':' to use no reference areas).
+ # (regression.sh sets $REF_PATH to a subdirectory itself.)
+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
+-	REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
++check test: samtools $(BUILT_TEST_PROGRAMS)
++	REF_PATH=: test/test.pl --exec bgzip=bgzip
+ 	test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+ 	test/merge/test_pretty_header
+ 	test/merge/test_rtrans_build
+@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
+ misc/wgsim: misc/wgsim.o
+ 	$(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
+ 
+-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
++misc/ace2sam.o: misc/ace2sam.c
+ misc/md5.o: misc/md5.c misc/md5.h
+-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
+-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
++misc/md5fa.o: misc/md5fa.c misc/md5.h
++misc/wgsim.o: misc/wgsim.c
+ 
+ misc/maq2sam-short.o: misc/maq2sam.c
+ 	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild
new file mode 100644
index 000000000000..7f596efe1100
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.1.ebuild,v 1.1 2015/01/06 12:57:48 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+	sys-libs/ncurses
+	~sci-libs/htslib-${PV}"
+
+RDEPEND="${CDEPEND}
+	dev-lang/lua
+	dev-lang/perl"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	find htslib-* -delete || die
+
+	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+	epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+	tc-export CC AR
+
+	sed \
+		-e '/htslib.mk/d' \
+		-i Makefile || die
+
+}
+
+src_compile() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		)
+	emake "${mymakeargs[@]}"
+}
+
+src_test() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		)
+	emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+	dobin samtools $(find misc -type f -executable)
+
+	python_replicate_script "${ED}"/usr/bin/varfilter.py
+	dolib.so libbam.so*
+
+	insinto /usr/include/bam
+	doins *.h
+
+	doman ${PN}.1
+	dodoc AUTHORS NEWS README
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples
+	fi
+}