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

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

[Martin Mokrejs]

commit:     b6828a1b578163ed6a480edf37e14e5928fefbf3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 22:26:25 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 22:26:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6828a1b

sci-biology/hmmer: version bump

Package-Manager: portage-2.2.18

 sci-biology/hmmer/ChangeLog              |  9 +++++++
 sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 46 ++++++++++++++++++++++++++++++++
 sci-biology/hmmer/metadata.xml           |  9 +++++++
 3 files changed, 64 insertions(+)

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
new file mode 100644
index 0000000..dcf8f5f
--- /dev/null
+++ b/sci-biology/hmmer/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/hmmer
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*hmmer-3.1_beta2 (19 Nov 2015)
+
+  19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +hmmer-3.1_beta2.ebuild, +metadata.xml:
+  sci-biology/hmmer: version bump

diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
new file mode 100644
index 0000000..2e266af
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+MY_PV="3.1b2"
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+HOMEPAGE="http://hmmer.janelia.org/"
+SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/"${MY_PV}"/"${PN}"-"${MY_PV}".tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs"
+KEYWORDS="~amd64"
+
+DEPEND="
+	mpi? ( virtual/mpi )
+	gsl? ( >=sci-libs/gsl-1.12 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-fix_tests.patch \
+		"${FILESDIR}"/${P}-perl-5.16-2.patch
+}
+
+src_configure() {
+	econf \
+		$(use_enable cpu_flags_x86_sse sse) \
+		$(use_enable mpi) \
+		$(use_enable threads) \
+		$(use_with gsl)
+}
+
+src_install() {
+	default
+
+	use static-libs && dolib.a src/libhmmer.a easel/libeasel.a
+
+	insinto /usr/share/${PN}
+	doins -r tutorial
+	dodoc Userguide.pdf
+}

diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
new file mode 100644
index 0000000..66fa766
--- /dev/null
+++ b/sci-biology/hmmer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<use>
+		<flag name="pvm">Add support for parallel virtual machine
+    (<pkg>sys-cluster/pvm</pkg>)</flag>
+	</use>
+</pkgmetadata>

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

[Martin Mokrejs]

commit:     e54f578fb268cd86700085e2d514fa69fd2115ec
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 22:42:06 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 22:42:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e54f578f

sci-biology/hmmer: fix ${S} variable

Package-Manager: portage-2.2.18

 sci-biology/hmmer/ChangeLog              | 4 ++++
 sci-biology/hmmer/hmmer-3.1_beta2.ebuild | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index dcf8f5f..71062a0 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  hmmer-3.1_beta2.ebuild:
+  sci-biology/hmmer: fix ${S} variable
+
 *hmmer-3.1_beta2 (19 Nov 2015)
 
   19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
index 2e266af..880df1e 100644
--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
+++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
@@ -21,6 +21,8 @@ DEPEND="
 	gsl? ( >=sci-libs/gsl-1.12 )"
 RDEPEND="${DEPEND}"
 
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-fix_tests.patch \

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

[Justin Lecher]

commit:     05eb7a24f10bde1d57544704961dff301645c34a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 09:27:59 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 09:27:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=05eb7a24

sci-biology/hmmer: drop unused local USE

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/hmmer/metadata.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index a6a17ef..8417d15 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -5,8 +5,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<use>
-		<flag name="pvm">Add support for parallel virtual machine
-    (<pkg>sys-cluster/pvm</pkg>)</flag>
-	</use>
 </pkgmetadata>