diff options
Diffstat (limited to 'sci-biology/wise')
| -rw-r--r-- | sci-biology/wise/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/wise/files/wise-api.tex.patch | 38 | ||||
| -rw-r--r-- | sci-biology/wise/wise-2.4.0_alpha-r1.ebuild | 71 | ||||
| -rw-r--r-- | sci-biology/wise/wise-2.4.0_alpha.ebuild | 73 |
4 files changed, 111 insertions, 74 deletions
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest index 36db61e514cd..5c4fc9140392 100644 --- a/sci-biology/wise/Manifest +++ b/sci-biology/wise/Manifest @@ -1,4 +1,5 @@ +AUX wise-api.tex.patch 2166 BLAKE2B 94cb69ddb9b751cf1efd7d4b98520144dc067c0dae83b2431d35f40c29d2c1d915335c610711f4a7225b3838991f8abce3bb9502aa8d540157afaddb5f389d70 SHA512 e01a902b46f00d6219d549f355b3e1f4373585baf104ff9a2193d6ac981e0aa277b0162307e0c3da17587e10138ad848da5439a0d407266c38f1ab8c7bedca4c DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c -EBUILD wise-2.4.0_alpha.ebuild 1737 BLAKE2B 29ae17532ef9a4919db09b4f6b71b92f3b89d1a03b75b1ce90a1defe49ea9d572d9e902620a6d267ad8fc77506a25fda84ede0804f4f0676ba8a0eb41df049c9 SHA512 b73b8fd3a78cdcdda2c39326bbd4dfd99c2828c38ae78537b33c8ea50291323841d0d348eb2b6965cfe1986d808f26ef83e115715fa7c14e31cb7a7e337d867c +EBUILD wise-2.4.0_alpha-r1.ebuild 1409 BLAKE2B 317764cdd23ecd59b6eeddcfe3efdab6a358a65a33166b504a98c05f7919864c7670e4c8516b70c98f85957ca4e9aff9700e75f6559e1718663b8535b2df6d89 SHA512 1c4910efb4a82c2ae703220cfdcf4fd9e51a38d23aa29e111559cc604d51185dd584fc33d473eec0fcd80ba177ced507eac230e4c60b589ef12f968a5aefe772 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..d6d56888dfb3 --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- a/api.tex.old ++++ b/api.tex +@@ -204,7 +204,7 @@ + \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) + \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins + \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) +-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) ++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) + \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) + \end{itemize} + +@@ -213,7 +213,7 @@ + \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) + \item Make a protein database from the single protein object (\ref{object_ProteinDB}) + \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) +-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) ++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) + \item Show the Hscore object using a show function (\ref{object_Hscore}) + \item Retrieve individual protein objects from the database by taking out the + DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object +@@ -232,7 +232,7 @@ + \item Read in a codon table (\ref{object_CodonTable}) + \item Make a random DNA model (\ref{object_RandomModelDNA}) + \item Make an algorithm type (\ref{module_gwrap}) +-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) ++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) + \item Run the actual algorithm (\ref{module_gwrap}) + \item show the alignment using genedisplay (\ref{module_gwrap}) + \end{itemize} +@@ -5055,7 +5055,7 @@ + Member functions of RandomModel + + \section{sequence\_codon} +-\label{module_sequence\_codon} ++\label{module_sequence_codon} + This module only contains factory methods + + \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild new file mode 100644 index 000000000000..a033ffd011bb --- /dev/null +++ b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +MY_PV="${PV/_}" +MY_P="${PN}${MY_PV}" +DESCRIPTION="Intelligent algorithms for DNA searches" +HOMEPAGE="http://www.ebi.ac.uk/Wise2/" +SRC_URI=" + ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${MY_P}.tar.gz + https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2 +" +S="${WORKDIR}"/${MY_P} + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND="${RDEPEND}" +BDEPEND=" + app-shells/tcsh + dev-lang/perl + virtual/latex-base +" + +PATCHES=( + "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch + "${WORKDIR}"/${P}-patchset/${P}-cflags.patch +) + +src_prepare() { + default + cd docs || die + cat ../src/models/*.tex ../src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die + cat wise2api.tex temp.tex apiend.tex > api.tex || die + eapply "${FILESDIR}"/${PN}-api.tex.patch +} + +src_compile() { + tc-export CC + emake -C src all + + if use doc; then + cd docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin src/bin/* src/dynlibsrc/testgendb + + insinto /usr/share/${PN} + doins -r wisecfg + + use doc && dodoc docs/*.ps + newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise +} diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild deleted file mode 100644 index c37a8972e84e..000000000000 --- a/sci-biology/wise/wise-2.4.0_alpha.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch toolchain-funcs versionator - -DESCRIPTION="Intelligent algorithms for DNA searches" -HOMEPAGE="http://www.ebi.ac.uk/Wise2/" -SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz - https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc static-libs" - -RDEPEND="~sci-biology/hmmer-2.3.2" -DEPEND=" - ${RDEPEND} - app-shells/tcsh - dev-lang/perl - virtual/latex-base" - -S="${WORKDIR}"/${PN}$(delete_version_separator 3) - -src_prepare() { - epatch \ - "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \ - "${WORKDIR}"/${P}-patchset/${P}-cflags.patch - cd "${S}"/docs || die - cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die - cat wise2api.tex temp.tex apiend.tex > api.tex || die - epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch -} - -src_compile() { - emake \ - -C src \ - CC="$(tc-getCC)" \ - all - if use doc; then - cd "${S}"/docs || die - for i in api appendix dynamite wise2 wise3arch; do - latex ${i} || die - latex ${i} || die - dvips ${i}.dvi -o || die - done - fi -} - -src_test() { - cd "${S}"/src || die - WISECONFIGDIR="${S}/wisecfg" emake test -} - -src_install() { - dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb - use static-libs && \ - dolib.a \ - "${S}"/src/base/libwisebase.a \ - "${S}"/src/dynlibsrc/libdyna.a \ - "${S}"/src/models/libmodel.a - - insinto /usr/share/${PN} - doins -r "${S}"/wisecfg - - if use doc; then - insinto /usr/share/doc/${PF} - doins "${S}"/docs/*.ps - fi - newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file" -} |