diff options
author | Justin Lecher <jlec@gentoo.org> | 2015-01-06 12:57:49 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2015-01-06 12:57:49 +0000 |
commit | 29a16e14da52bacb7d7763c066efdf14a6f722a7 (patch) | |
tree | bb650f1fae77066800a207590fa2cf11fffb7a6f /sci-biology/samtools | |
parent | Convert to python-single-r1, enforce a match on Python version used by vim. (diff) | |
download | historical-29a16e14da52bacb7d7763c066efdf14a6f722a7.tar.gz historical-29a16e14da52bacb7d7763c066efdf14a6f722a7.tar.bz2 historical-29a16e14da52bacb7d7763c066efdf14a6f722a7.zip |
sci-biology/samtools: Version BUmp
Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!
Diffstat (limited to 'sci-biology/samtools')
-rw-r--r-- | sci-biology/samtools/ChangeLog | 10 | ||||
-rw-r--r-- | sci-biology/samtools/Manifest | 33 | ||||
-rw-r--r-- | sci-biology/samtools/files/samtools-1.1-buildsystem.patch | 153 | ||||
-rw-r--r-- | sci-biology/samtools/samtools-1.1.ebuild | 83 |
4 files changed, 262 insertions, 17 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/Manifest b/sci-biology/samtools/Manifest index c8da084205e3..b4bc3f5d31a8 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -3,31 +3,34 @@ Hash: SHA512 AUX samtools-0.1.19-buildsystem.patch 6227 SHA256 44c6e4df3ceb36e539716350ef10e0f4e348d524c5dfdb96ad7c9ccbed9570d0 SHA512 dd41a0ab20ad216273f38b42e6abafd70378bcf966403379e73d08c93e92f04ee79dae07baf7f626b30d57deea29d56a729928c18c5d012d950cfe10912adf3d WHIRLPOOL 9ba69f11b8071fe1c9a3269a482e1de0c6563a0a94b96bcef97a1442a6e4d594aea55b4e1c75381b6ed792e7e3e3809da80c9b8a22ec74af63c14315a51e9771 AUX samtools-1.0-buildsystem.patch 1672 SHA256 fe82984a2475ce4666bd386bb6f1ab9aff4e6402dc02e671171f41ad082345c1 SHA512 b75a9c6a57fa5f4c4dc9eda529eb500f1828c6e0910922ac34869c0972661a4fa51a65b83a153905a090b4f67e0bb7a9316ecc33b04a09a46c74d2bd67c84cf6 WHIRLPOOL eb72243b5e2376df4c417e0b171eb3f71c11ca842014fc72f75463a4bebde11771484049a12650e9169f1c4ba390699af99ebf63d6459b4cc673195b273bedcc +AUX samtools-1.1-buildsystem.patch 7030 SHA256 a4751ad60699c18c081ced0fa4f5bd494ad072bcc73147d16cf90b35aa9b0bca SHA512 cb0190cfb0d31a9feef068df285734d218b05dcc3b4fae95cb31007ed513986a571d4e0533e918b503c9e3d1fbef18af5c7371294218a5fd0e8837eda56c854a WHIRLPOOL b450a1d971f9e443b14c4a555d6cf43b3e6fc20c4a24ecba32faef47fbb4fbac49260feb92f056d54824721db787295bec3b5a682cec2c7dd6d5c0d1d0157b0b DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5 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 EBUILD samtools-0.1.12.ebuild 827 SHA256 7f8dec32073313ec5a0a7801bcaf7675d74f4eefb2478b19615b22f1bd7e3708 SHA512 b67feeb1909327b6ab19fdb3167e602ab01bd075685bded200109b5def4ad80353f39c77dd8c8e1de1b6a43482acc0b85626951503f42f6dbf416bdbbf740851 WHIRLPOOL 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SHA512 84b937c3b5143a84a8d9c2062e4e3b91b8a4fe5a50be379ce0dfecba19fc1735a90b1f7690762c7a33aede06229ff229e84a3c31a704ae56cb2241be33a88002 WHIRLPOOL ccc11832e93be31003f41fcd6789537f4c1cf16e0972f0d6cfcd6ef0dc4ee18e4d34907c8f5c32a84137f9bcc5bde2f5d7ea3e61d39e837b4bf0f2319930bb11 -MISC ChangeLog 3931 SHA256 20f76948927192c6d06843b709a3a22be2b17ff580b5cabad5c9540a0901ed29 SHA512 c028a7c6409305a80c359372d3cff855eb4776f34f5b4f2381375a986ceb9ce1e066597af93cfd38a2772be5483baeed139b571fe2d22cdc76898c3a50e8498b WHIRLPOOL ea4608633e47883f2e4c60f4330827e17fb3da3d7f6aba65ee5d0f44ded74e13a7188e402e56505f7ca7afb0dec4d8e122ae20cda6a53a8876ae49a08b7169ec +EBUILD samtools-1.1.ebuild 1780 SHA256 7939d37f2dfea1a0f190a57bc02374a8787d4e6a21325677b6c175bc42e19561 SHA512 14be9b8002b38f2fe6f7f0c01629ada05539cba20476436f2de691cb8a73f8751e66045e81dc5aa01cb1fe7d2971cb660e6cc66c9191eba71bc3d87741b3a7b5 WHIRLPOOL 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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 +} |