diff options
Diffstat (limited to 'sci-biology/fasta')
| -rw-r--r-- | sci-biology/fasta/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/fasta/fasta-36.3.8h-r1.ebuild | 12 | ||||
| -rw-r--r-- | sci-biology/fasta/fasta-36.3.8i.ebuild | 81 |
3 files changed, 91 insertions, 6 deletions
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index 1626943dfb25..e2d6df08a8af 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1,4 +1,6 @@ AUX fasta-36.3.8h-ldflags.patch 2291 BLAKE2B 61c0b7d82a4c138e82148f354576fbeadf38362337ae6d2ecdb23aea5c4dbb3719f3889a0479ea2b48de8e2c3e19c5b61a7b9508507fd7f61289205b93e899ed SHA512 a34021b398e077a409bd31508b0736e7a0fda533d86b26efe998227ce628414796a0dfd88b0010154e25ef79148b1b9acac4cd94cb7aa72a59fbcbd1fbbb6726 DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391 -EBUILD fasta-36.3.8h-r1.ebuild 1713 BLAKE2B de1276ea990e856cf562a5f970d180c3872c3ce6d3d8f73a50b398ff1408f7840872d90e690a9511cdbb14c586627c061389ad307c85b1a2662130aea66d0b33 SHA512 059b00c917565477765897b03656dfe8e67c2879ac8a78b2187edd0a5f0199f52dca45886dd8d2ac300ee0995697458fffa69e7704df951837b1c50d7ad92f9d +DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234 +EBUILD fasta-36.3.8h-r1.ebuild 1770 BLAKE2B 77f3ebcfa44b0dd96b73909ea5cfe772366985e688df007aed3205a159d5896c6be20e88ab9e294920e55452014db1f73c2fc9d0d0763c7e5bba53e89e99dc44 SHA512 d55d8345400033078b9d7e634bbf4881f2e69bb3e3c4f048f840cc44ac90af844496070836b21fd208203f98ef4cb80b0b256ccdd9a0674d83d8fef2f3398b18 +EBUILD fasta-36.3.8i.ebuild 1725 BLAKE2B 28655f72b4eccad925599f3811ba2ff86e5ea5a9d9eb90a37f1545269dea5549a47972044e41bf5e515faca12d2c42856d64439c4077419d69051bcdee168076 SHA512 0c4320a3238c93743e111864dccf73312abadd84f51a4ca8793c4d98a28e5b95185ce0f15d3c7c37ab4962e25898e8234acca1c27d4467bc9a9439ffdfd7df16 MISC metadata.xml 344 BLAKE2B 75f42620d20abfbba91acae49acb672fe1b42fccf6227e358c1d94101c894226f51e9c2efe4014dd263b55a2940894eee9d8c96fb5ac6ff64c3c4ae6a426cc74 SHA512 13001db79cb9763ee83f1701e316287efdaef1ac5c4eab1249a1815df5ac6a34ff6b0f76e1706684058966b2201c642a2f8bda1d6d36473c0cdfbe00ca1d094a diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild index 1cd7ca60dcde..b811765e502e 100644 --- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild +++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -15,10 +15,7 @@ S="${WORKDIR}/${PN}36-${MY_PV}" LICENSE="fasta" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="debug cpu_flags_x86_sse2 test" -RESTRICT="!test? ( test )" - -BDEPEND="test? ( app-shells/tcsh )" +IUSE="debug cpu_flags_x86_sse2" src_prepare() { CC_ALT= @@ -45,6 +42,11 @@ src_prepare() { export CC_ALT="${CC_ALT}" export ALT="${ALT}" + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862267 + # https://github.com/wrpearson/fasta36/issues/63 + filter-lto + eapply "${FILESDIR}"/${P}-ldflags.patch sed \ diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild b/sci-biology/fasta/fasta-36.3.8i.ebuild new file mode 100644 index 000000000000..6363b4b56f2d --- /dev/null +++ b/sci-biology/fasta/fasta-36.3.8i.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +MY_PV="${PV}_14-Nov-2020" + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}36-${MY_PV}" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="debug cpu_flags_x86_sse2" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ "$(tc-getCC)" == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT="$(tc-getCC)" + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862267 + # https://github.com/wrpearson/fasta36/issues/63 + filter-lto + + sed \ + -e 's:-ffast-math::g' \ + -i make/Makefile* || die + + eapply_user +} + +src_compile() { + emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all +} + +src_test() { + cd test || die + FASTLIBS="../conf" bash test.sh || die +} + +src_install() { + dobin bin/* + + pushd bin >/dev/null || die + local i + for i in *36; do + dosym ${i} /usr/bin/${i%36} + done + popd >/dev/null || die + + insinto /usr/share/${PN} + doins -r conf/. data seq + + doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} + dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*} +} |