gentoo resync : 26.08.2021

12 files changed, 141 insertions, 115 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 1be341788cfa..ef5ed336ca9a 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index faf3dab4cfed..160f7b2aef62 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1,4 +1,4 @@
-AUX mb_readline_312.patch 1108 BLAKE2B 4413b4193ee7c0c51a1ad7a422474f137682151f932b28fc6ee98390a228a4e5bbabcf30f3d78fc56a79a665ffc40bf05376fbbf14b68ff43bc10a9001ec8e6e SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114
+AUX mb_readline_312.patch 586 BLAKE2B 6505a8d9fc40c0470264b6e293f2f4e51a5d6b4a73dfeaff747e2f4acd122369d810cdc86ae0d7cead3a3741cfffc02080c07618c2847985553322a1c9bf79b5 SHA512 8427c83ccb98c0b57274914d8f0d0f539ace7dbc475eb10bd586762efa3465b595b91907b55d6809b94e6b9c4f65aa139bc16a7d81b1c76f7623eae46d495aa8
 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
-EBUILD mrbayes-3.1.2-r2.ebuild 1344 BLAKE2B f0b52d8b615dabe59d1d1e2dedbeb3f86513127fd3b2112783e64c38b812a3a998f5b33c397b7d9f1b333ed58bcc8ecdce8d5d5c4f73d2abe29ba631c3929d48 SHA512 d64b835015f70b4c28c3bfe37438be5e27c42b4546e24f8f4c40089f9ca98d5b29b7340fa88efa7fb9f764cb46c4396ced213ca9d35c3d64f33454b6a4854f9b
+EBUILD mrbayes-3.1.2-r2.ebuild 1346 BLAKE2B 282f7f2bf6abb8370b5a007a8e680009f3f5e8e839d7817a1cb3b83e515b2909d5a9c7aa3eae6355ab59c4e1e2e4b9a7f8694076d50b019232fa367cd93df231 SHA512 60541b7af0243c4263d302d69ea38c6f1fcee96739eba121a48bf42e2b46f210efa971d65d0d517ed6b383fb6ce337008b13655c4f52e2783d456a04b43b9eb7
 MISC metadata.xml 916 BLAKE2B 511d932eff0de935a1c8634cc6398bfe6cceb7f2766534e5486f5ff2aa4c900b8d48d7dabc5cee2506061c36421f0ef336f43b5df5d23a03ab5911a1fef87b1b SHA512 ab6be2e4111088bc13e6da5f65d11437dc05dbcdeab83e5d3899b913ff9ad3dc1f22ec81f2fe73f60bf991d01f0a8691eaa124ba24bd7ebb17d995fdd271bfef
diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch
index 2f8bab1e7665..d41986704708 100644
--- a/sci-biology/mrbayes/files/mb_readline_312.patch
+++ b/sci-biology/mrbayes/files/mb_readline_312.patch
@@ -1,25 +1,13 @@
-Index: Makefile
-===================================================================
-RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v
-retrieving revision 3.23
-retrieving revision 3.24
-diff -U2 -r3.23 -r3.24
---- Makefile	22 Dec 2005 16:13:06 -0000	3.23
-+++ Makefile	3 Jan 2006 16:43:13 -0000	3.24
+--- a/Makefile
++++ b/Makefile
 @@ -50,4 +50,5 @@
  ifeq  ($(strip $(USEREADLINE)),yes)
      CFLAGS += -DUSE_READLINE
 +#   CFLAGS += -DCOMPLETIONMATCHES
  	LIBS += -lncurses -lreadline 
  endif
-Index: bayes.c
-===================================================================
-RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v
-retrieving revision 3.39
-retrieving revision 3.40
-diff -U2 -r3.39 -r3.40
---- bayes.c	23 Dec 2005 16:26:28 -0000	3.39
-+++ bayes.c	3 Jan 2006 16:43:13 -0000	3.40
+--- a/bayes.c
++++ b/bayes.c
 @@ -382,9 +382,11 @@
  char **readline_completion(const char *text, int start, int stop) {
  	char **matches = (char **) NULL;
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
index ecc44fe43454..cee9e0f2d286 100644
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -1,26 +1,29 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Bayesian Inference of Phylogeny"
 HOMEPAGE="http://mrbayes.csit.fsu.edu/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 
-SLOT="0"
 LICENSE="GPL-2"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 IUSE="debug mpi readline"
 
 DEPEND="
-	sys-libs/ncurses:0=
+	sys-libs/ncurses:=
 	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline:0= )"
+	readline? ( sys-libs/readline:= )
+"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
+	default
+
 	if use mpi; then
 		sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support."
 	fi
@@ -30,7 +33,7 @@ src_prepare() {
 	else
 		# Only needed for OSX with an old (4.x) version of
 		# libreadline, but it doesn't hurt for other distributions.
-		epatch "${FILESDIR}"/mb_readline_312.patch
+		eapply "${FILESDIR}"/mb_readline_312.patch
 	fi
 	sed -e 's:-ggdb::g' -i Makefile || die
 }
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
index c7a81385ede8..ba6392685d12 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 1131 BLAKE2B 48e491bcd929d9e126bcc26d1d4c60c8bd6f036ba0b7e8fe0824eece4ad7a4b7c4681918c9dc12af5f247a77b3675fad3dfb10e7fc1152dbb5b651993eb03c4a SHA512 f2058ddd233397fffc694be06cc683020a620a4239e864f5abd1d14456c50fbc11721bd649b4c80185991cb954ddf308edc394ef88e966fa0200435c8f1e8c29
+EBUILD plink-1.90_pre140514.ebuild 1165 BLAKE2B 0b8e58c958acde62b0f59fd81917b088ec997ab877e1c8d83fe917d9d2df5b715a9634d5f69c1263a51090829a8eaa88a553e2980bbcc6d3b6936336705af03e SHA512 c73fccf66c5d11a72657985172c8fbf1b89107fd46a519474dad167f1279c0f6a976b0096e3d550fb2b9835980aa02ad81c68a819b3aec036faf60b341acf9d2
 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 578881ac0f59..2595c3ab7983 100644
--- a/sci-biology/plink/plink-1.90_pre140514.ebuild
+++ b/sci-biology/plink/plink-1.90_pre140514.ebuild
@@ -1,36 +1,36 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
 inherit toolchain-funcs
 
 DESCRIPTION="Whole genome association analysis toolset"
 HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
 SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip"
+S="${WORKDIR}"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 RDEPEND="
 	sys-libs/zlib
 	virtual/cblas
 	virtual/lapack
 "
-DEPEND="
-	${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
 	app-arch/unzip
 	virtual/pkgconfig
 "
 
-S="${WORKDIR}/"
-
 # Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
 # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
 
 src_prepare() {
+	default
+
 	sed \
 		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
 		-i *.{c,h} || die
@@ -47,6 +47,7 @@ src_compile() {
 	emake \
 		CXX=$(tc-getCXX) \
 		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
 		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
 		BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
 }
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index c1f07d33f7b9..7698aa2dbbc3 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,3 +1,3 @@
 DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
-EBUILD velvet-1.2.10.ebuild 2096 BLAKE2B 3a85f8e1a24af2e9794be70bfe691f7df2e2321619af96b5fcac5b8b0d445b96d258b2b9cd6d4474e05fb60559fc1e3015229d1fc933378974ec795129f15aed SHA512 96bc66027211a3700bcac197fc7c2de3bec34b44f5a39bee4ef7d25f2247617351fca293ebfde1c64f4b7931b41cc5bda87515a3b05d1fe5d308d3879fabe89d
+EBUILD velvet-1.2.10.ebuild 2085 BLAKE2B f0aa88a145341553ad74006189dec738a05a29620a4f90843daf4f4e3fd2bce857836b1332c2fee4764db63a202c6b5a908f97dd7ae1e654f24c51e04c865065 SHA512 4a61a2df8715691deba0dfb22b6e8ca049e655e55e82e620a25af4de625b6e43757963942304983145c9b7a29751dbc90aa3854fdb9496a50622d4b5b0d677ed
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
index b4d8ae8641b2..ea0b3630b78b 100644
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -1,28 +1,25 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
 inherit flag-o-matic toolchain-funcs
 
-MY_P=${PN}_${PV}
-
+MY_P="${PN}_${PV}"
 DESCRIPTION="A sequence assembler for very short reads"
 HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
 SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+S="${WORKDIR}"/${MY_P}
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc openmp"
 
-RDEPEND=""
-DEPEND="${RDEPEND}
-	doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
+BDEPEND="doc? ( virtual/latex-base )"
 
 src_prepare() {
+	default
 	if ! use doc; then
 		sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
 	fi
@@ -48,7 +45,7 @@ src_prepare() {
 	tc-export CC
 
 	MAKE_XOPTS=(
-		CC=$(tc-getCC)
+		CC="$(tc-getCC)"
 		CFLAGS="${CFLAGS}"
 		OPT="${CFLAGS}"
 	)
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"
-}