From deaa21ff2b928318d0e1b8fe45aa404411f08086 Mon Sep 17 00:00:00 2001 From: David Seifert Date: Mon, 28 Mar 2016 01:52:51 +0200 Subject: sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions Package-Manager: portage-2.2.28 --- .../files/samtools-0.1.20-buildsystem.patch | 20 +++---- sci-biology/samtools/samtools-0.1.20-r1.ebuild | 70 ++++++++++++++++++++++ sci-biology/samtools/samtools-0.1.20.ebuild | 70 ---------------------- 3 files changed, 80 insertions(+), 80 deletions(-) create mode 100644 sci-biology/samtools/samtools-0.1.20-r1.ebuild delete mode 100644 sci-biology/samtools/samtools-0.1.20.ebuild (limited to 'sci-biology') diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch index dfdd890b1087..eb9f6934a96f 100644 --- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch +++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch @@ -75,15 +75,15 @@ .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur -lib:libbam.a -+lib:libbam-legacy.a ++lib:libbam-0.1-legacy.a -libbam.a:$(LOBJS) -+libbam-legacy.a:$(LOBJS) ++libbam-0.1-legacy.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-legacy.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread razip:razip.o razf.o $(KNETFILE_O) - $(CC) $(CFLAGS) -o $@ $^ -lz @@ -105,21 +105,21 @@ -libbam.1.dylib-local:$(LOBJS) - libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz -+libbam-legacy.1.dylib-local:$(LOBJS) -+ libtool -dynamic $(LOBJS) -o libbam-legacy.1.dylib -lc -lz ++libbam-0.1-legacy.1.dylib-local:$(LOBJS) ++ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz -libbam.so.1-local:$(LOBJS) - $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+libbam-legacy.so.1-local:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-legacy.so -o libbam-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread ++libbam-0.1-legacy.so.1-local:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread dylib: @$(MAKE) cleanlocal; \ case `uname` in \ - Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ - Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ -+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.so.1-local;; \ -+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-legacy.1.dylib-local;; \ ++ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \ ++ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \ *) echo 'Unknown OS';; \ esac @@ -162,7 +162,7 @@ bamcheck:bamcheck.o - $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-legacy -lpthread -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c diff --git a/sci-biology/samtools/samtools-0.1.20-r1.ebuild b/sci-biology/samtools/samtools-0.1.20-r1.ebuild new file mode 100644 index 000000000000..744d15ff5771 --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.20-r1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0.1-legacy" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="sys-libs/ncurses:0= + dev-lang/lua:0 + dev-lang/perl" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-buildsystem.patch" +) + +src_prepare() { + default + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + tc-export CC AR +} + +src_compile() { + local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" + emake dylib LIBCURSES="${_ncurses}" + emake LIBCURSES="${_ncurses}" +} + +src_install() { + dobin samtools $(find bcftools misc -type f -executable) + mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die + mkdir "${ED}"/usr/bin || die + mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die + + mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die + python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py + + dolib.so libbam-${SLOT}$(get_libname 1) + dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) + + insinto /usr/include/bam-${SLOT} + doins *.h + + mv ${PN}{,-${SLOT}}.1 || die + doman ${PN}-${SLOT}.1 + dodoc AUTHORS NEWS + + use examples && dodoc -r examples +} + +pkg_postinst() { + elog "This version of samtools should *not* be your first choice for working" + elog "with NGS data. It is installed solely for programs requiring it." + elog "It is recommended that you use >=sci-biology/samtools-1.2." +} diff --git a/sci-biology/samtools/samtools-0.1.20.ebuild b/sci-biology/samtools/samtools-0.1.20.ebuild deleted file mode 100644 index 3ee9956f3759..000000000000 --- a/sci-biology/samtools/samtools-0.1.20.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils python-r1 toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="legacy" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="examples" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="sys-libs/ncurses:0= - dev-lang/lua:0 - dev-lang/perl" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}/${P}-buildsystem.patch" -) - -src_prepare() { - default - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die - tc-export CC AR -} - -src_compile() { - local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" - emake dylib LIBCURSES="${_ncurses}" - emake LIBCURSES="${_ncurses}" -} - -src_install() { - dobin samtools $(find bcftools misc -type f -executable) - mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die - mkdir "${ED}"/usr/bin || die - mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die - - mv "${ED}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die - python_replicate_script "${ED}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py - - dolib.so libbam-${SLOT}$(get_libname 1) - dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) - - insinto /usr/include/bam-${SLOT} - doins *.h - - mv ${PN}{,-${SLOT}}.1 || die - doman ${PN}-${SLOT}.1 - dodoc AUTHORS NEWS - - use examples && dodoc -r examples -} - -pkg_postinst() { - elog "This version of samtools should *not* be your first choice for working" - elog "with NGS data. It is installed solely for programs requiring it." - elog "It is recommended that you use >=sci-biology/samtools-1.2." -} -- cgit v1.2.3-65-gdbad