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commit: 6a6b5309daa23e0dbb6318512e68e81ffa668c81 |
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Author: Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr> |
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AuthorDate: Sun Aug 22 19:37:25 2021 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Aug 22 19:37:25 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6a6b5309 |
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|
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sci-biology/wise: Port to EAPI 8 |
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|
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Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr> |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/wise/files/wise-api.tex.patch | 38 +++++++++++++++ |
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sci-biology/wise/wise-2.4.0_alpha-r1.ebuild | 71 ++++++++++++++++++++++++++++ |
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sci-biology/wise/wise-2.4.0_alpha.ebuild | 73 ----------------------------- |
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3 files changed, 109 insertions(+), 73 deletions(-) |
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|
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diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch |
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new file mode 100644 |
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index 00000000000..d6d56888dfb |
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--- /dev/null |
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+++ b/sci-biology/wise/files/wise-api.tex.patch |
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@@ -0,0 +1,38 @@ |
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+--- a/api.tex.old |
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++++ b/api.tex |
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+@@ -204,7 +204,7 @@ |
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+ \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) |
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+ \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins |
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+ \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) |
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+-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) |
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++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) |
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+ \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) |
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+ \end{itemize} |
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+ |
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+@@ -213,7 +213,7 @@ |
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+ \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) |
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+ \item Make a protein database from the single protein object (\ref{object_ProteinDB}) |
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+ \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) |
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+-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) |
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++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) |
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+ \item Show the Hscore object using a show function (\ref{object_Hscore}) |
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+ \item Retrieve individual protein objects from the database by taking out the |
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+ DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object |
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+@@ -232,7 +232,7 @@ |
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+ \item Read in a codon table (\ref{object_CodonTable}) |
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+ \item Make a random DNA model (\ref{object_RandomModelDNA}) |
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+ \item Make an algorithm type (\ref{module_gwrap}) |
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+-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) |
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++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) |
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+ \item Run the actual algorithm (\ref{module_gwrap}) |
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+ \item show the alignment using genedisplay (\ref{module_gwrap}) |
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+ \end{itemize} |
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+@@ -5055,7 +5055,7 @@ |
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+ Member functions of RandomModel |
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+ |
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+ \section{sequence\_codon} |
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+-\label{module_sequence\_codon} |
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++\label{module_sequence_codon} |
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+ This module only contains factory methods |
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+ |
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+ \subsection{sequence\_codon factory methods} |
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|
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diff --git a/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild |
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new file mode 100644 |
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index 00000000000..a033ffd011b |
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--- /dev/null |
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+++ b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild |
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@@ -0,0 +1,71 @@ |
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+# Copyright 1999-2021 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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+inherit toolchain-funcs |
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+ |
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+MY_PV="${PV/_}" |
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+MY_P="${PN}${MY_PV}" |
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+DESCRIPTION="Intelligent algorithms for DNA searches" |
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+HOMEPAGE="http://www.ebi.ac.uk/Wise2/" |
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+SRC_URI=" |
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+ ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${MY_P}.tar.gz |
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+ https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2 |
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+" |
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+S="${WORKDIR}"/${MY_P} |
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+ |
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+LICENSE="BSD" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="doc" |
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+ |
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+RDEPEND="~sci-biology/hmmer-2.3.2" |
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+DEPEND="${RDEPEND}" |
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+BDEPEND=" |
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+ app-shells/tcsh |
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+ dev-lang/perl |
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+ virtual/latex-base |
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+" |
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+ |
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+PATCHES=( |
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+ "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch |
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+ "${WORKDIR}"/${P}-patchset/${P}-cflags.patch |
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+) |
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+ |
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+src_prepare() { |
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+ default |
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+ cd docs || die |
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+ cat ../src/models/*.tex ../src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die |
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+ cat wise2api.tex temp.tex apiend.tex > api.tex || die |
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+ eapply "${FILESDIR}"/${PN}-api.tex.patch |
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+} |
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+ |
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+src_compile() { |
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+ tc-export CC |
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+ emake -C src all |
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+ |
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+ if use doc; then |
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+ cd docs || die |
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+ for i in api appendix dynamite wise2 wise3arch; do |
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+ latex ${i} || die |
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+ latex ${i} || die |
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+ dvips ${i}.dvi -o || die |
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+ done |
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+ fi |
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+} |
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+ |
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+src_test() { |
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+ cd src || die |
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+ WISECONFIGDIR="${S}/wisecfg" emake test |
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+} |
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+ |
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+src_install() { |
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+ dobin src/bin/* src/dynlibsrc/testgendb |
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+ |
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+ insinto /usr/share/${PN} |
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+ doins -r wisecfg |
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+ |
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+ use doc && dodoc docs/*.ps |
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+ newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise |
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+} |
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|
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diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild |
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deleted file mode 100644 |
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index c37a8972e84..00000000000 |
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--- a/sci-biology/wise/wise-2.4.0_alpha.ebuild |
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+++ /dev/null |
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@@ -1,73 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=5 |
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- |
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-inherit epatch toolchain-funcs versionator |
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- |
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-DESCRIPTION="Intelligent algorithms for DNA searches" |
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-HOMEPAGE="http://www.ebi.ac.uk/Wise2/" |
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-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz |
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- https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" |
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- |
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-LICENSE="BSD" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="doc static-libs" |
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- |
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-RDEPEND="~sci-biology/hmmer-2.3.2" |
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-DEPEND=" |
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- ${RDEPEND} |
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- app-shells/tcsh |
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- dev-lang/perl |
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- virtual/latex-base" |
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- |
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-S="${WORKDIR}"/${PN}$(delete_version_separator 3) |
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- |
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-src_prepare() { |
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- epatch \ |
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- "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \ |
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- "${WORKDIR}"/${P}-patchset/${P}-cflags.patch |
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- cd "${S}"/docs || die |
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- cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die |
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- cat wise2api.tex temp.tex apiend.tex > api.tex || die |
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- epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch |
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-} |
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- |
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-src_compile() { |
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- emake \ |
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- -C src \ |
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- CC="$(tc-getCC)" \ |
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- all |
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- if use doc; then |
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- cd "${S}"/docs || die |
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- for i in api appendix dynamite wise2 wise3arch; do |
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- latex ${i} || die |
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- latex ${i} || die |
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- dvips ${i}.dvi -o || die |
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- done |
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- fi |
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-} |
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- |
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-src_test() { |
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- cd "${S}"/src || die |
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- WISECONFIGDIR="${S}/wisecfg" emake test |
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-} |
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- |
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-src_install() { |
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- dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb |
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- use static-libs && \ |
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- dolib.a \ |
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- "${S}"/src/base/libwisebase.a \ |
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- "${S}"/src/dynlibsrc/libdyna.a \ |
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- "${S}"/src/models/libmodel.a |
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- |
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- insinto /usr/share/${PN} |
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- doins -r "${S}"/wisecfg |
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- |
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- if use doc; then |
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- insinto /usr/share/doc/${PF} |
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- doins "${S}"/docs/*.ps |
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- fi |
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- newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file" |
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-} |