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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2011-06-24 17:09 Justin Lecher
  0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
  To: gentoo-commits

commit:     05abe2253162a6c232112729cca4c64da4dc5470
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 12:55:21 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 12:55:21 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=05abe225

Sort inherit and/or USE

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/wcd/wcd-0.6.0_beta.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-biology/wcd/wcd-0.6.0_beta.ebuild b/sci-biology/wcd/wcd-0.6.0_beta.ebuild
index f7fbd75..c51852e 100644
--- a/sci-biology/wcd/wcd-0.6.0_beta.ebuild
+++ b/sci-biology/wcd/wcd-0.6.0_beta.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit flag-o-matic eutils
+inherit eutils flag-o-matic
 
 DESCRIPTION="wcd clusters sequences (typically ESTs) by either of: d2 function, edit distance, common word heuristics."
 HOMEPAGE="http://code.google.com/p/wcdest"



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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2011-06-25 17:22 Justin Lecher
  0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2011-06-25 17:22 UTC (permalink / raw
  To: gentoo-commits

commit:     d04e6ced91a19a3d4cb2081b8fa33f86b0507d30
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 14:34:20 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 14:34:20 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d04e6ced

Cleaned ebuild

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/wcd/ChangeLog             |   10 ++++++
 sci-biology/wcd/wcd-0.6.0.ebuild      |   52 +++++++++++++++++++++++++++++++++
 sci-biology/wcd/wcd-0.6.0_beta.ebuild |   47 -----------------------------
 3 files changed, 62 insertions(+), 47 deletions(-)

diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
new file mode 100644
index 0000000..19bb05d
--- /dev/null
+++ b/sci-biology/wcd/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/wcd
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*wcd-0.6.0 (25 Jun 2011)
+
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild,
+  +wcd-0.6.0.ebuild:
+  Cleaned ebuild
+

diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.0.ebuild
new file mode 100644
index 0000000..3367cc4
--- /dev/null
+++ b/sci-biology/wcd/wcd-0.6.0.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils flag-o-matic
+
+DESCRIPTION="Sequence clustering by either of: d2 function, edit distance, common word heuristics"
+HOMEPAGE="http://code.google.com/p/wcdest/"
+SRC_URI="http://wcdest.googlecode.com/files/${P}B.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="doc mpi threads"
+
+DEPEND="mpi? ( sys-cluster/mpich2 )"
+RDEPEND=""
+
+S="${WORKDIR}"/wcd-0.6.0
+
+src_configure(){
+	local myconf=""
+	if use mpi; then
+		myconf="${myconf} --enable-mpi"
+	fi
+
+	if use threads; then
+		myconf="${myconf} --enable-pthreads"
+	fi
+
+	econf ${myconf}
+}
+
+src_compile() {
+	emake
+	if use doc; then
+		emake pdf info html
+	fi
+}
+
+src_install() {
+	local f
+	emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install
+
+	if use doc; then
+		for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do
+			dodoc ${f}
+		done
+	fi
+}

diff --git a/sci-biology/wcd/wcd-0.6.0_beta.ebuild b/sci-biology/wcd/wcd-0.6.0_beta.ebuild
deleted file mode 100644
index c51852e..0000000
--- a/sci-biology/wcd/wcd-0.6.0_beta.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="wcd clusters sequences (typically ESTs) by either of: d2 function, edit distance, common word heuristics."
-HOMEPAGE="http://code.google.com/p/wcdest"
-SRC_URI="http://wcdest.googlecode.com/files/wcd-0.6.0B.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="mpi threads"
-
-DEPEND="mpi? ( sys-cluster/mpich2 )"
-RDEPEND=""
-
-S="${WORKDIR}"/wcd-0.6.0
-
-src_prepare(){
-	mv "${DESTDIR}"/wcd-0.6.0B.tar.gz "${DESTDIR}"/wcd-0.6.0.tar.gz || die
-}
-	
-src_compile(){
-	local myconf=""
-	if use mpi; then
-		myconf="${myconf} --enable-mpi"
-	fi
-
-	if use threads; then
-		myconf="${myconf} --enable-pthreads"
-	fi
-
-	econf ${myconf} || die
-
-	emake || die
-	emake pdf || die
-	emake info || die
-	emake html || die
-}
-
-src_install() {
-	emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install \
-		|| die "make install failed"
-	for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do dodoc ${f} || die; done
-}



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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-01-09 15:30 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-01-09 15:30 UTC (permalink / raw
  To: gentoo-commits

commit:     5742accf45fcfa12220b7ff21f6b633f0423ed04
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan  9 15:29:10 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan  9 15:29:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5742accf

sci-biology/wcd: version bump, clarify package description, add comments about addons

Package-Manager: portage-2.2.7

---
 sci-biology/wcd/ChangeLog                              | 10 ++++++++--
 sci-biology/wcd/{wcd-0.6.0.ebuild => wcd-0.6.3.ebuild} | 12 +++++++++---
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index be44eea..359dd42 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-biology/wcd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*wcd-0.6.3 (09 Jan 2015)
+
+  09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +wcd-0.6.3.ebuild,
+  -wcd-0.6.0.ebuild:
+  sci-biology/wcd: version bump, clarify package description, add comments about
+  addons
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> wcd-0.6.0.ebuild,
   +files/wcd-0.6.0-impl-decl.patch, +files/wcd-0.6.0-ldflags.patch,
   metadata.xml:
@@ -13,4 +20,3 @@
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild,
   +wcd-0.6.0.ebuild:
   Cleaned ebuild
-

diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
similarity index 63%
rename from sci-biology/wcd/wcd-0.6.0.ebuild
rename to sci-biology/wcd/wcd-0.6.3.ebuild
index eb906dc..87c5c51 100644
--- a/sci-biology/wcd/wcd-0.6.0.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -8,9 +8,9 @@ AUTOTOOLS_AUTORECONF=true
 
 inherit autotools-utils flag-o-matic multilib
 
-DESCRIPTION="Sequence clustering by either of: d2 function, edit distance, common word heuristics"
+DESCRIPTION="EST sequence clustering by either of: d2 function, edit distance, common word heuristics"
 HOMEPAGE="http://code.google.com/p/wcdest/"
-SRC_URI="http://wcdest.googlecode.com/files/${P}B.tar.gz -> ${P}.tar.gz"
+SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -43,3 +43,9 @@ 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)
 }
+
+# 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=


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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-12-02 22:35 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-12-02 22:35 UTC (permalink / raw
  To: gentoo-commits

commit:     7397eb0576d2a41c5b2f70124cedb67aff2fd9e0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec  2 22:34:35 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec  2 22:34:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7397eb05

sci-biology/wcd: fix S

Package-Manager: portage-2.2.26

 sci-biology/wcd/ChangeLog        | 3 +++
 sci-biology/wcd/wcd-0.6.3.ebuild | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index 40aa5ce..7fd7947 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild:
+  sci-biology/wcd: fix S
+
 *wcd-0.6.3 (09 Jan 2015)
 
   09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +wcd-0.6.3.ebuild,

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
index b09fdcd..2910efe 100644
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -12,6 +12,8 @@ DESCRIPTION="EST sequence clustering by either of: d2 function, edit distance, c
 HOMEPAGE="http://code.google.com/p/wcdest/"
 SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz -> ${P}.tar.gz"
 
+S="${WORKDIR}"/wcd-express-"${PV}"
+
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~x86 ~amd64"


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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-12-02 23:48 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-12-02 23:48 UTC (permalink / raw
  To: gentoo-commits

commit:     5322770db7dd1062b01b9401aafdb5f98c32f3be
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec  2 23:47:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec  2 23:47:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5322770d

sci-biology/wcd: also install some documentation, albeit probably old

Package-Manager: portage-2.2.26

 sci-biology/wcd/ChangeLog        | 3 +++
 sci-biology/wcd/wcd-0.6.3.ebuild | 5 ++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index 761945d..5d9d88f 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild:
+  sci-biology/wcd: also install some documentation, albeit probably old
+
   02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   +files/wcd-0.6.3-impl-decl.patch, +files/wcd-0.6.3-ldflags.patch,
   -files/wcd-0.6.0-impl-decl.patch, -files/wcd-0.6.0-ldflags.patch:

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
index 2910efe..98850ed 100644
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -10,7 +10,9 @@ inherit autotools-utils flag-o-matic multilib
 
 DESCRIPTION="EST sequence clustering by either of: 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 -> ${P}.tar.gz"
+SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${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}"
 
@@ -44,6 +46,7 @@ src_compile() {
 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


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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-12-02 23:56 Martin Mokrejs
  0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-12-02 23:56 UTC (permalink / raw
  To: gentoo-commits

commit:     e27e1fed06d64d8e83d19858b9674ac111f04ce7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec  2 23:55:42 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec  2 23:55:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e27e1fed

sci-biology/wcd: add note on supported MPI implementations

Package-Manager: portage-2.2.26

 sci-biology/wcd/ChangeLog        | 3 +++
 sci-biology/wcd/wcd-0.6.3.ebuild | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index 5d9d88f..7336100 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -3,6 +3,9 @@
 # $Id$
 
   02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild:
+  sci-biology/wcd: add note on supported MPI implementations
+
+  02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild:
   sci-biology/wcd: also install some documentation, albeit probably old
 
   02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
index 98850ed..e09b302 100644
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -21,6 +21,8 @@ SLOT="0"
 KEYWORDS="~x86 ~amd64"
 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=""
 


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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-12-03 10:57 Justin Lecher
  0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2015-12-03 10:57 UTC (permalink / raw
  To: gentoo-commits

commit:     fdc3b49e0b790d9eda465c994a6a0a0323836b88
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  3 10:57:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 10:57:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdc3b49e

sci-biology/wcd: Chop DESCRIPTION to 80 chars

Package-Manager: portage-2.2.25
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/wcd/wcd-0.6.3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
index 3d7c1fc..47374fe 100644
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -8,7 +8,7 @@ AUTOTOOLS_AUTORECONF=true
 
 inherit autotools-utils flag-o-matic multilib
 
-DESCRIPTION="EST sequence clustering by either of: d2 function, edit distance, common word heuristics"
+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


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2015-12-03 10:57 Justin Lecher
  0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2015-12-03 10:57 UTC (permalink / raw
  To: gentoo-commits

commit:     bf9f376cd9a6767cf5377e19b49058f244780698
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  3 10:56:43 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 10:56:43 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf9f376c

sci-biology/wcd: Drop bundled precompiled object files

Package-Manager: portage-2.2.25
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/wcd/wcd-0.6.3.ebuild | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
index e09b302..3d7c1fc 100644
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3.ebuild
@@ -31,6 +31,11 @@ PATCHES=(
 	"${FILESDIR}"/${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 )


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* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2021-01-18 12:42 Andrew Ammerlaan
  0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 12:42 UTC (permalink / raw
  To: gentoo-commits

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.*
+}


^ permalink raw reply related	[flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2021-01-18 12:50 Andrew Ammerlaan
  0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 12:50 UTC (permalink / raw
  To: gentoo-commits

commit:     fbeb6e10e31db43d7640709a9727601952dac1c4
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:50:40 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:50:40 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fbeb6e10

sci-biology/wcd: add missing trailing slash

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_p20180430.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
index 740deddba..e295296ec 100644
--- a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
+++ b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
@@ -43,6 +43,6 @@ src_compile() {
 
 src_install() {
 	use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
-	emake install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
+	emake install PREFIX=/usr LIBDIR="${D}"/usr/$(get_libdir)
 	dodoc "${DISTDIR}"/wcd.*
 }


^ permalink raw reply related	[flat|nested] 10+ messages in thread
end of thread, other threads:[~2021-01-18 12:50 UTC | newest]

Thread overview: 10+ messages (download: mbox.gz follow: Atom feed
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2015-12-03 10:57 [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/ Justin Lecher
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2021-01-18 12:50 Andrew Ammerlaan
2021-01-18 12:42 Andrew Ammerlaan
2015-12-03 10:57 Justin Lecher
2015-12-02 23:56 Martin Mokrejs
2015-12-02 23:48 Martin Mokrejs
2015-12-02 22:35 Martin Mokrejs
2015-01-09 15:30 Martin Mokrejs
2011-06-25 17:22 Justin Lecher
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