commit: 35ac52402ad5f6a417d6af10e13df64a8da559b2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 16 23:02:54 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 16 23:02:54 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=35ac5240
sci-biology/samtools: version bump; partially updated patch but without
libbam.{a,so} change
I did not manage to get to compile the shared library so samtools binary at the
moment
contains libbam.a (which is what upstream prefers but not Gentoo).
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../files/samtools-1.3.1-buildsystem.patch | 75 +++++++++++++++++++
sci-biology/samtools/samtools-1.3.1.ebuild | 84 ++++++++++++++++++++++
2 files changed, 159 insertions(+)
diff --git a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
new file mode 100644
index 000000000..bd0f20c7c
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
@@ -0,0 +1,75 @@
+--- samtools-1.3.1/Makefile.ori 2016-04-22 11:51:16.000000000 +0200
++++ samtools-1.3.1/Makefile 2017-02-16 23:41:19.819951687 +0100
+@@ -21,9 +21,9 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
++CC ?= gcc
+ CPPFLAGS =
+-CFLAGS = -g -Wall -O2
++CFLAGS ?= -g -Wall -O2
+ LDFLAGS =
+ LIBS =
+
+@@ -197,8 +203,8 @@
+ # 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_rtrans_build
+ test/merge/test_trans_tbl_init
+@@ -210,28 +216,28 @@
+ test/split/test_parse_args
+
+
+-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
sam_opts.o $(HTSLIB)
++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o
test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o
$(HTSLIB)
++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o
sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o
$(HTSLIB)
++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o
sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o
$(HTSLIB)
++test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o
test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/split/test_expand_format_string: test/split/test_expand_format_string.o
test/test.o sam_opts.o $(HTSLIB)
++test/split/test_expand_format_string: test/split/test_expand_format_string.o
test/test.o sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@
test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB)
$(ALL_LIBS)
+
+-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o
test/test.o sam_opts.o $(HTSLIB)
++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o
test/test.o sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o
test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/split/test_parse_args: test/split/test_parse_args.o test/test.o
sam_opts.o $(HTSLIB)
++test/split/test_parse_args: test/split/test_parse_args.o test/test.o
sam_opts.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o
test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
++test/vcf-miniview: test/vcf-miniview.o
+ $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB)
$(ALL_LIBS)
+
+ test_test_h = test/test.h $(htslib_sam_h)
+@@ -258,10 +264,10 @@
+ misc/maq2sam-long: misc/maq2sam-long.o
+ $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
+
+-misc/md5fa: misc/md5fa.o $(HTSLIB)
++misc/md5fa: misc/md5fa.o
+ $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+-misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
++misc/md5sum-lite: misc/md5sum-lite.o
+ $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
+
+ misc/wgsim: misc/wgsim.o
diff --git a/sci-biology/samtools/samtools-1.3.1.ebuild
b/sci-biology/samtools/samtools-1.3.1.ebuild
new file mode 100644
index 000000000..8c118dcf4
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.3.1.ebuild
@@ -0,0 +1,84 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)"
+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="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses:0=
+ >=sci-libs/htslib-${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"
+ )
+ LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ #dolib.so libbam.so*
+ dolib libbam.a
+
+ 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
+}
