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

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

[Martin Mokrejs]

commit:     71cdc2ea8a2ce9b5fbf6aaf315c1d7c7016805b9
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr  1 20:46:38 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr  1 20:46:38 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=71cdc2ea

sci-biology/diamond: new package

Do not know if the SSE instruction calls can be protected
with CPU_FLAGS or similar. See page 2 in diamond_manual.pdf .

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/diamond/diamond-0.9.19.ebuild | 27 +++++++++++++++++++++++++++
 sci-biology/diamond/metadata.xml          | 12 ++++++++++++
 2 files changed, 39 insertions(+)

diff --git a/sci-biology/diamond/diamond-0.9.19.ebuild b/sci-biology/diamond/diamond-0.9.19.ebuild
new file mode 100644
index 000000000..fde9b9080
--- /dev/null
+++ b/sci-biology/diamond/diamond-0.9.19.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs cmake-utils
+
+DESCRIPTION="Alternative of blastp/blastx searches using DNA short reads through protein db"
+HOMEPAGE="http://ab.inf.uni-tuebingen.de/software/diamond
+	https://github.com/bbuchfink/diamond"
+SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz"
+# EGIT_REPO_URI="https://github.com/bbuchfink/diamond.git"
+
+LICENSE="AGPL-3" # diamond_manual.pdf says AGPL but src/COPYING used to say BSD?
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# uses SSE instructions, SSSE3 and POPCNT
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+# use cmake -DBUILD_STATIC=ON to create a statically linked binary
+src_install(){
+	cmake-utils_src_install
+	dodoc README.rst diamond_manual.pdf
+}

diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/diamond/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

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

[Andrew Ammerlaan]

commit:     67d31ee6311a1bc7720142feb053f9477ef4d04e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:18:33 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:18:33 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=67d31ee6

sci-biology/diamond: properly name tarball

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

 sci-biology/diamond/diamond-0.9.19.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/diamond/diamond-0.9.19.ebuild b/sci-biology/diamond/diamond-0.9.19.ebuild
index fde9b9080..a2044cfbc 100644
--- a/sci-biology/diamond/diamond-0.9.19.ebuild
+++ b/sci-biology/diamond/diamond-0.9.19.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -8,7 +8,7 @@ inherit toolchain-funcs cmake-utils
 DESCRIPTION="Alternative of blastp/blastx searches using DNA short reads through protein db"
 HOMEPAGE="http://ab.inf.uni-tuebingen.de/software/diamond
 	https://github.com/bbuchfink/diamond"
-SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz"
+SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 # EGIT_REPO_URI="https://github.com/bbuchfink/diamond.git"
 
 LICENSE="AGPL-3" # diamond_manual.pdf says AGPL but src/COPYING used to say BSD?

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

[Andrew Ammerlaan]

commit:     ac1b8a1ca47e0b4dbc063bbd9f6d5945ed723e73
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:17:43 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:17:43 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac1b8a1c

sci-biology/diamond: version bump 2.0.6, cmake-utils --> cmake

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../{diamond-0.9.19.ebuild => diamond-2.0.6.ebuild}       | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/sci-biology/diamond/diamond-0.9.19.ebuild b/sci-biology/diamond/diamond-2.0.6.ebuild
similarity index 73%
rename from sci-biology/diamond/diamond-0.9.19.ebuild
rename to sci-biology/diamond/diamond-2.0.6.ebuild
index a2044cfbc..1ec499917 100644
--- a/sci-biology/diamond/diamond-0.9.19.ebuild
+++ b/sci-biology/diamond/diamond-2.0.6.ebuild
@@ -1,27 +1,18 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit toolchain-funcs cmake-utils
+inherit cmake
 
 DESCRIPTION="Alternative of blastp/blastx searches using DNA short reads through protein db"
 HOMEPAGE="http://ab.inf.uni-tuebingen.de/software/diamond
 	https://github.com/bbuchfink/diamond"
 SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-# EGIT_REPO_URI="https://github.com/bbuchfink/diamond.git"
 
 LICENSE="AGPL-3" # diamond_manual.pdf says AGPL but src/COPYING used to say BSD?
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
-# uses SSE instructions, SSSE3 and POPCNT
-
-DEPEND=""
-RDEPEND="${DEPEND}"
 
+# uses SSE instructions, SSSE3 and POPCNT
 # use cmake -DBUILD_STATIC=ON to create a statically linked binary
-src_install(){
-	cmake-utils_src_install
-	dodoc README.rst diamond_manual.pdf
-}