* [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"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [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
-}
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [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=
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [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"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [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
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [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=""
^ 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 )
^ 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: 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 -> ${P}.tar.gz
http://www.bioinf.wits.ac.za/~scott/wcd.html
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/
@ 2021-01-18 12:42 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 12:42 UTC (permalink / raw
To: gentoo-commits
commit: 54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:42:29 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:42:29 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=54f544dd
sci-biology/wcd: fix fetch
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/wcd/wcd-0.6.3.ebuild | 62 ------------------------------
sci-biology/wcd/wcd-0.6.3_p20180430.ebuild | 48 +++++++++++++++++++++++
2 files changed, 48 insertions(+), 62 deletions(-)
diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
deleted file mode 100644
index d4b797608..000000000
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic multilib
-
-DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
-HOMEPAGE="http://code.google.com/p/wcdest/"
-SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${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]
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2015-01-09 15:30 [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/ Martin Mokrejs
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2015-12-03 10:57 Justin Lecher
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2015-12-02 23:56 Martin Mokrejs
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2011-06-25 17:22 Justin Lecher
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