From 34dea8e38f88007799629d0a56b12dec480b1d21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 20 Jun 2021 14:45:01 +0100 Subject: gentoo resync : 20.06.2021 --- sci-biology/mira/Manifest | 2 +- sci-biology/mira/mira-4.0.2-r1.ebuild | 97 +++++++++++++++++++++++++++++++++++ sci-biology/mira/mira-4.0.2.ebuild | 97 ----------------------------------- 3 files changed, 98 insertions(+), 98 deletions(-) create mode 100644 sci-biology/mira/mira-4.0.2-r1.ebuild delete mode 100644 sci-biology/mira/mira-4.0.2.ebuild (limited to 'sci-biology/mira') diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest index ca5165677704..e26af9ae8615 100644 --- a/sci-biology/mira/Manifest +++ b/sci-biology/mira/Manifest @@ -3,5 +3,5 @@ AUX mira-4.0.2-cmath.patch 295 BLAKE2B 30892b3a519682db7e04b1a0169c4018d7f4dd4e3 AUX mira-4.0.2-cout.patch 735 BLAKE2B d386a704829b7f3264ee69d55d7451a5479a9d121e49cbd8d9322c9a27a065073076608569d169982784fcc6cc4ae4423712d15d1c4d642a6b8fd0dd7d5fe3a3 SHA512 9d1aa493d20481d0a7e3eaefba36dc29d7903f70c9a445b6e0ea478d04124e8a81de37c437f0fb28c0a395562db7e78217cf09e500fd4a1f2a1f929c1d4d2a5a DIST mira-4.0.2.tar.bz2 10368046 BLAKE2B cc84c6c13c8024409634ccafd103be8a4f2a9e27fa7f19d2ef401393db9e8063a6fac2f21cd25dfe58e90aee8cf38983369d928241f9bc65e78da0e95fa41d3b SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b -EBUILD mira-4.0.2.ebuild 2558 BLAKE2B de1f15bf2fc98b4f7487d2a354a319a335357f0decd483ea01584c7de9a4fbddb0717415e4cdd7552865768decb52763d6bbd869c39f8a9461c9349eb8299846 SHA512 65f3ae83abe4f97cb21b16157dbbd172b7c4780eb414acbf1c337bad2890899bd0cc35d0d1e7f51d4e328563f2cdbe0314f8883216c6ccfc6fdb40a4664ba8d0 +EBUILD mira-4.0.2-r1.ebuild 2563 BLAKE2B 7cfb5eb182024af1ef2dc73de85909bdfe57cb95bb1af557c64e2f9ee002eb3363360b27283d8cc31105bd97d4b4fca2d70830bcd02c983402773793c0696409 SHA512 a4783d30af6224c0931370e05d932ea0a98a08487b3036d75b43a303063b575772a385b1ea54758a80987cfcff39512bd506b383178413fb8dfe542b87adbfca MISC metadata.xml 355 BLAKE2B 2557fbd5c3427ccced7fc6d233954a3e9d4297c0bec17158997f4f7fb490b525235ae27fff1ed19113b596de77a23518505e20531c7e40020e3f54932f5d9e6f SHA512 9d9037805b94622cb468553fa27c948de2849ac4c6dc1eafae8c3261554b5e97b631fe77e4e589eff613822d316b2843bcab0c47547b202651c8a804a516554e diff --git a/sci-biology/mira/mira-4.0.2-r1.ebuild b/sci-biology/mira/mira-4.0.2-r1.ebuild new file mode 100644 index 000000000000..cbd1309c474f --- /dev/null +++ b/sci-biology/mira/mira-4.0.2-r1.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MIRA_3RDPARTY_PV="06-07-2012" +MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) + +inherit autotools multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI=" + https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 +# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +CDEPEND=" + dev-libs/boost:=[threads(+)] + dev-util/google-perftools" +DEPEND="${CDEPEND} + sys-devel/flex + app-editors/vim-core + dev-libs/expat" +RDEPEND="${CDEPEND}" + +#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED +# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) +DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) + +PATCHES=( + "${FILESDIR}/${PN}-4.0.2-boost-1.50.patch" + "${FILESDIR}/${PN}-4.0.2-cout.patch" + "${FILESDIR}/${PN}-4.0.2-cmath.patch" +) + +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + + default + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf + + # Remove C++ source files that upstream built with flex. + local f + local PREBUILT_CXX_LEXER_FILES=( + "${S}"/src/caf/caf_flexer.cc + "${S}"/src/io/exp_flexer.cc + "${S}"/src/mira/parameters_flexer.cc + ) + + for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do + if [[ -f ${f} ]] ; then + rm "${f}" || die "Failed to remove ${f}" + else + die "${f} not found" + fi + done +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-thread=boost_thread-mt +} + +#src_compile() { +# base_src_compile +# # TODO: resolve docbook incompatibility for building docs +# use doc && emake -C doc clean docs +#} + +src_install() { + default + + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} + dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} +} + +pkg_postinst() { + einfo "Documentation is no longer built, you can find it at:" + einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" +} diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild deleted file mode 100644 index c37fa2333129..000000000000 --- a/sci-biology/mira/mira-4.0.2.ebuild +++ /dev/null @@ -1,97 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - -inherit autotools multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina" -HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI=" - https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -S="${WORKDIR}"/"${PN}"-"${MY_PV}" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="doc" - -CDEPEND=" - dev-libs/boost[threads] - dev-util/google-perftools" -DEPEND="${CDEPEND} - sys-devel/flex - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) - -PATCHES=( - "${FILESDIR}/${PN}-4.0.2-boost-1.50.patch" - "${FILESDIR}/${PN}-4.0.2-cout.patch" - "${FILESDIR}/${PN}-4.0.2-cmath.patch" -) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - - default - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - eautoreconf - - # Remove C++ source files that upstream built with flex. - local f - local PREBUILT_CXX_LEXER_FILES=( - "${S}"/src/caf/caf_flexer.cc - "${S}"/src/io/exp_flexer.cc - "${S}"/src/mira/parameters_flexer.cc - ) - - for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do - if [[ -f ${f} ]] ; then - rm "${f}" || die "Failed to remove ${f}" - else - die "${f} not found" - fi - done -} - -src_configure() { - econf \ - --with-boost="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-thread=boost_thread-mt -} - -#src_compile() { -# base_src_compile -# # TODO: resolve docbook incompatibility for building docs -# use doc && emake -C doc clean docs -#} - -src_install() { - default - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} -- cgit v1.2.3