diff options
-rw-r--r-- | sci-biology/samtools/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch | 75 | ||||
-rw-r--r-- | sci-biology/samtools/samtools-1.3.1.ebuild | 84 |
3 files changed, 160 insertions, 0 deletions
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 867b5820b..0ee32c7cf 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,3 +1,4 @@ DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 +DIST samtools-1.3.1.tar.bz2 4030072 SHA256 6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e SHA512 3bd702d3e922a18843ab47dcc9c545d747b7d2ce74a8ae02c3f6e3a5972af54ce0ad5103f0e2f8658e57d908e14e93740d5c63ab8ab728f813ae440d63eb8a29 WHIRLPOOL 1aaee2521e5c7b4740996d585c77a328d17c68363cd81a48140402a5bd82c0987f9ddcf79c8c9842b92ebe994860c7f650fe49e60d964a037ba72853ece95245 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 +} |