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/Manifest.gz | Bin 22137 -> 22136 bytes sci-biology/mira/Manifest | 2 +- sci-biology/mira/mira-4.0.2-r1.ebuild | 97 ++++++++++++ sci-biology/mira/mira-4.0.2.ebuild | 97 ------------ sci-biology/ncbi-tools/Manifest | 2 +- sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild | 167 -------------------- sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 +++++++++++++++++++++ sci-biology/plink/Manifest | 2 +- sci-biology/plink/plink-1.90_pre140514.ebuild | 10 +- 9 files changed, 275 insertions(+), 271 deletions(-) create mode 100644 sci-biology/mira/mira-4.0.2-r1.ebuild delete mode 100644 sci-biology/mira/mira-4.0.2.ebuild delete mode 100644 sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild create mode 100644 sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 5f89a213cf0b..b4d35e4c4285 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ 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" -} diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest index 7bbabc7adc05..c32f0222f1b9 100644 --- a/sci-biology/ncbi-tools/Manifest +++ b/sci-biology/ncbi-tools/Manifest @@ -6,5 +6,5 @@ AUX ncbi-tools-extra_vib.patch 1393 BLAKE2B 3c9e0ffa614e7baccf87beea601561a8f6e1 AUX ncbi-tools-lop.patch 701 BLAKE2B 9df2fd3ba86bc9a4f52d3c1809b4d795392666c601aa607d2377129c42562a99087387eaa69d9e9ae07545ea91808902db65718ccf3d671ca88f7255119b1028 SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352 AUX ncbirc 57 BLAKE2B 140c208cf1c7dbb6a204e58632c576e4edf0cd71d151b69f70839f1b06ae19db0d74d49179d2f0bc1320a40fabad49bed18a98a8bd2a75f6ecf068e647382c60 SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 -EBUILD ncbi-tools-2.2.26-r2.ebuild 4631 BLAKE2B 0a31d2096d49f16b8a5c4a2220fe55aa40557cc33b6a7fa5d4136f86fa0008d24e089b725fa6a12609475c3cbd58c7f379c65a77eab6c957fc811110d60f64f5 SHA512 7d9a4e2dfd3edaa28e36f8caf223b794fb37306270177bfa383f952b96799b177fd68f2688cd79fb81d85801d17d5f9e01faf3d7c8978d77372260b81d95d992 +EBUILD ncbi-tools-2.2.26-r3.ebuild 4660 BLAKE2B ef1a3d2e1751792d2726786309eab8b514c72391c2362ce4927659012c96a991531ff558916d69ab89745259bdaceb75a794cff850deec817a90a3c0c5752804 SHA512 7fbb34e5f2ff5f4615b3f41834643acb89e3f47378301f90a449bee6d8629be6c057c4a04c320c10cc2b867ab13b7eae187b73ff987abaf31e03729e2eca11c2 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild deleted file mode 100644 index 2a3668a82a53..000000000000 --- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch flag-o-matic prefix toolchain-funcs - -DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" -HOMEPAGE="https://www.ncbi.nlm.nih.gov/" -SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="public-domain" -KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc static-libs X" - -RDEPEND=" - app-shells/tcsh - dev-lang/perl - media-libs/libpng:0= - X? ( - media-libs/fontconfig - x11-libs/motif:0= - x11-libs/libICE - x11-libs/libX11 - x11-libs/libXft - x11-libs/libXmu - x11-libs/libXt - )" -DEPEND=" - ${RDEPEND} - virtual/pkgconfig -" - -S="${WORKDIR}/ncbi" - -EXTRA_VIB="asn2all asn2asn" - -pkg_setup() { - echo - ewarn 'Please note that the NCBI toolkit (and especially the X' - ewarn 'applications) are known to have compilation and run-time' - ewarn 'problems when compiled with agressive compilation flags. The' - ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' - ewarn 'X support is enabled.' - echo -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-extra_vib.patch \ - "${FILESDIR}"/${P}-bfr-overflow.patch \ - "${FILESDIR}"/${P}-format-security.patch \ - "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch - - if use ppc || use ppc64; then - epatch "${FILESDIR}"/${PN}-lop.patch - fi - - if ! use X; then - sed \ - -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ - -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ - -i "${S}"/make/makedis.csh || die - else - # X applications segfault on startup on x86 with -O3. - use x86 || replace-flags '-O3' '-O2' - fi - - # Apply user C flags... - cd "${S}"/platform - sed \ - -e "s:-O[s0-9]\?::g" \ - -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ - -e 's:-x[A-Z]*::g' \ - -e 's:-pipe::g' \ - -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ - -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ - -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ - -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ - -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ - -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ - -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ - -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ - -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ - -i * || die - - # We use dynamic libraries - sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die - - sed \ - -re "s:/usr(/bin/.*sh):\1:g" \ - -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ - -i $(find "${S}" -type f) || die -} - -src_compile() { - export EXTRA_VIB - cd "${WORKDIR}" - csh ncbi/make/makedis.csh || die - mkdir "${S}"/cgi "${S}"/real || die - mv "${S}"/bin/*.cgi "${S}"/cgi || die - mv "${S}"/bin/*.REAL "${S}"/real || die - cd "${S}"/demo - emake \ - -f ../make/makenet.unx \ - CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ - LDFLAGS="${LDFLAGS}" \ - spidey - cp spidey ../bin/ || die -} - -src_install() { - #sci-geosciences/cdat-lite - mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die - - dobin "${S}"/bin/* - - for i in ${EXTRA_VIB}; do - dobin "${S}"/build/${i} - done - use static-libs && dolib.a "${S}"/lib/*.a - mkdir -p "${ED}"/usr/include/ncbi - cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ - die "Failed to install headers." - - # TODO: wwwblast with webapps - #insinto /usr/share/ncbi/lib/cgi - #doins ${S}/cgi/* - #insinto /usr/share/ncbi/lib/real - #doins ${S}/real/* - - # Basic documentation - dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} - newdoc "${S}"/doc/fa2htgs/README README.fa2htgs - newdoc "${S}"/config/README README.config - newdoc "${S}"/network/encrypt/README README.encrypt - newdoc "${S}"/network/nsclilib/readme README.nsclilib - newdoc "${S}"/sequin/README README.sequin - mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die - doman "${S}"/doc/man/* - - # Hypertext user documentation - dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} - insinto /usr/share/doc/${PF}/html - doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install - - # Developer documentation - if use doc; then - # Demo programs - mkdir "${ED}"/usr/share/ncbi - mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die - fi - - # Shared data (similarity matrices and such) and database directory. - insinto /usr/share/ncbi - doins -r "${S}"/data - dodir /usr/share/ncbi/formatdb - - # Default config file to set the path for shared data. - insinto /etc/ncbi - newins "${FILESDIR}"/ncbirc .ncbirc - eprefixify "${ED}"/etc/ncbi/.ncbirc - - # Env file to set the location of the config file and BLAST databases. - newenvd "${FILESDIR}"/21ncbi-r1 21ncbi -} diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild new file mode 100644 index 000000000000..cec2f688b661 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild @@ -0,0 +1,169 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit epatch flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" +HOMEPAGE="https://www.ncbi.nlm.nih.gov/" +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc static-libs X" + +RDEPEND=" + app-shells/tcsh + dev-lang/perl + media-libs/libpng:0= + virtual/glu + virtual/opengl + X? ( + media-libs/fontconfig + x11-libs/motif:0= + x11-libs/libICE + x11-libs/libX11 + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXt + )" +DEPEND=" + ${RDEPEND} + virtual/pkgconfig +" + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and especially the X' + ewarn 'applications) are known to have compilation and run-time' + ewarn 'problems when compiled with agressive compilation flags. The' + ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' + ewarn 'X support is enabled.' + echo +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-extra_vib.patch \ + "${FILESDIR}"/${P}-bfr-overflow.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + + if use ppc || use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + + if ! use X; then + sed \ + -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i "${S}"/make/makedis.csh || die + else + # X applications segfault on startup on x86 with -O3. + use x86 || replace-flags '-O3' '-O2' + fi + + # Apply user C flags... + cd "${S}"/platform + sed \ + -e "s:-O[s0-9]\?::g" \ + -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ + -e 's:-x[A-Z]*::g' \ + -e 's:-pipe::g' \ + -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ + -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ + -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ + -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ + -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ + -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ + -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -i * || die + + # We use dynamic libraries + sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die + + sed \ + -re "s:/usr(/bin/.*sh):\1:g" \ + -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ + -i $(find "${S}" -type f) || die +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + csh ncbi/make/makedis.csh || die + mkdir "${S}"/cgi "${S}"/real || die + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + cd "${S}"/demo + emake \ + -f ../make/makenet.unx \ + CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ + LDFLAGS="${LDFLAGS}" \ + spidey + cp spidey ../bin/ || die +} + +src_install() { + #sci-geosciences/cdat-lite + mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die + + dobin "${S}"/bin/* + + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} + done + use static-libs && dolib.a "${S}"/lib/*.a + mkdir -p "${ED}"/usr/include/ncbi + cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ + die "Failed to install headers." + + # TODO: wwwblast with webapps + #insinto /usr/share/ncbi/lib/cgi + #doins ${S}/cgi/* + #insinto /usr/share/ncbi/lib/real + #doins ${S}/real/* + + # Basic documentation + dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs + newdoc "${S}"/config/README README.config + newdoc "${S}"/network/encrypt/README README.encrypt + newdoc "${S}"/network/nsclilib/readme README.nsclilib + newdoc "${S}"/sequin/README README.sequin + mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die + doman "${S}"/doc/man/* + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} + insinto /usr/share/doc/${PF}/html + doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install + + # Developer documentation + if use doc; then + # Demo programs + mkdir "${ED}"/usr/share/ncbi + mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi + doins -r "${S}"/data + dodir /usr/share/ncbi/formatdb + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc + eprefixify "${ED}"/etc/ncbi/.ncbirc + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi +} diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest index f7bc93be9327..c7a81385ede8 100644 --- a/sci-biology/plink/Manifest +++ b/sci-biology/plink/Manifest @@ -1,3 +1,3 @@ DIST plink-1.90_pre140514.zip 822157 BLAKE2B 3c29670862de99c9715bc37d8cffc2b02c0cb25ad746975f253ca1e8094b24668cc6739943c68bfa407471f30835a74c6ad027eaa56a92f13445e0a02854cad3 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 -EBUILD plink-1.90_pre140514.ebuild 1119 BLAKE2B 71e5c5abf54d97212a1c21b722f12326052f4f01b0892e7aef288aa22ccc57075ab806268fd5d99b4d638e6ffba01ebeb86855596c038a9a84d72960cc98cf43 SHA512 2867a0d71b034886afef5adc81fe6e48b41b4f9a3dadd72b5286769388bcc7977688dc19eb27b52b6cfa9a952e249d7e876dd0547f455824dd972ce2011b6952 +EBUILD plink-1.90_pre140514.ebuild 1131 BLAKE2B 48e491bcd929d9e126bcc26d1d4c60c8bd6f036ba0b7e8fe0824eece4ad7a4b7c4681918c9dc12af5f247a77b3675fad3dfb10e7fc1152dbb5b651993eb03c4a SHA512 f2058ddd233397fffc694be06cc683020a620a4239e864f5abd1d14456c50fbc11721bd649b4c80185991cb954ddf308edc394ef88e966fa0200435c8f1e8c29 MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild index ab931553b923..578881ac0f59 100644 --- a/sci-biology/plink/plink-1.90_pre140514.ebuild +++ b/sci-biology/plink/plink-1.90_pre140514.ebuild @@ -14,14 +14,16 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND=" - app-arch/unzip - virtual/pkgconfig" RDEPEND=" sys-libs/zlib virtual/cblas virtual/lapack - " +" +DEPEND=" + ${RDEPEND} + app-arch/unzip + virtual/pkgconfig +" S="${WORKDIR}/" -- cgit v1.2.3