[gentoo-commits] proj/sci:master commit in: sci-biology/wcd/

["Andrew Ammerlaan" <andrewammerlaan@riseup.net>]

commit:     54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:42:29 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:42:29 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=54f544dd

sci-biology/wcd: fix fetch

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/wcd/wcd-0.6.3.ebuild           | 62 ------------------------------
 sci-biology/wcd/wcd-0.6.3_p20180430.ebuild | 48 +++++++++++++++++++++++
 2 files changed, 48 insertions(+), 62 deletions(-)

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
deleted file mode 100644
index d4b797608..000000000
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic multilib
-
-DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
-HOMEPAGE="http://code.google.com/p/wcdest/"
-SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinf.wits.ac.za/~scott/wcd.html
-	http://www.bioinf.wits.ac.za/~scott/wcd.pdf"
-
-S="${WORKDIR}"/wcd-express-"${PV}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc mpi threads"
-
-# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse,
-# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse)
-DEPEND="mpi? ( sys-cluster/mpich2 )"
-RDEPEND=""
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
-	"${FILESDIR}"/${P}-impl-decl.patch
-	)
-
-src_prepare() {
-	rm -r src/*o src/.deps || die
-	autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=()
-	use mpi && myeconfargs+=( --enable-mpi )
-
-	use threads && myeconfargs+=( --enable-pthreads )
-
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	use doc && autotools-utils_src_compile pdf info html
-}
-
-src_install() {
-	use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
-	autotools-utils_src_install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
-	dodoc "${DISTDIR}"/wcd.*
-}
-
-# consider providing the EMBOSS wrapper for wcd
-# https://code.google.com/p/wcdest/downloads/detail?name=wcd_emboss_wrap_001.tar.gz
-
-# also consider ESTsim
-# https://code.google.com/p/wcdest/downloads/detail?name=estsim_distrib.tar.gz&can=2&q=

diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
new file mode 100644
index 000000000..740deddba
--- /dev/null
+++ b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+COMMIT="aee525029bb661b633097e989c6fe2eaa93d2def"
+
+inherit multilib
+
+DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
+HOMEPAGE="https://shaze.github.io/wcdest/"
+SRC_URI="https://github.com/shaze/wcdest/archive/${COMMIT}.tar.gz -> ${P}.tar.gz
+	http://www.bioinf.wits.ac.za/~scott/wcd.html
+	http://www.bioinf.wits.ac.za/~scott/wcd.pdf"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+
+IUSE="doc mpi threads"
+
+# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse,
+# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse)
+DEPEND="mpi? ( sys-cluster/mpich2 )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-0.6.3-ldflags.patch
+	"${FILESDIR}"/${PN}-0.6.3-impl-decl.patch
+)
+
+S="${WORKDIR}/${PN}est-${COMMIT}/code"
+
+src_configure(){
+	econf \
+		$(use_enable mpi) \
+		$(use_enable threads pthreads)
+}
+
+src_compile() {
+	default
+	use doc && emake pdf info html
+}
+
+src_install() {
+	use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
+	emake install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
+	dodoc "${DISTDIR}"/wcd.*
+}