[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Martin Mokrejs]

commit:     601c9013c6e86a87af3ca3b3185c285bccdf90ce
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Mar 17 18:19:11 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 17 18:19:11 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=601c9013

sci-biology/minimap2: new package

Arguably we could do something about CPUFLAGS but as the
package compiles its for for all SSE2 up to SSE4.1 combinations
maybe we only should ensure -mtune and -march options
were filtered by the ebuild.

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/minimap2/metadata.xml         | 15 +++++++++++++++
 sci-biology/minimap2/minimap2-2.17.ebuild | 20 ++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/sci-biology/minimap2/metadata.xml b/sci-biology/minimap2/metadata.xml
new file mode 100644
index 000000000..c9e82c96a
--- /dev/null
+++ b/sci-biology/minimap2/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+	<upstream>
+		<remote-id type="github">minimap2</remote-id>
+	</upstream>
+</pkgmetadata>

diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild b/sci-biology/minimap2/minimap2-2.17.ebuild
new file mode 100644
index 000000000..e40058243
--- /dev/null
+++ b/sci-biology/minimap2/minimap2-2.17.ebuild
@@ -0,0 +1,20 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="splice-aware sequence aligner"
+HOMEPAGE="https://github.com/lh3/minimap2"
+SRC_URI="https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17.tar.bz2 -> ${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_install(){
+	dobin "${PN}"
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Andrew Ammerlaan]

commit:     010d62d1ee091d576e54e6b7781d668594c253a3
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 19:53:16 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 19:53:16 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=010d62d1

sci-biology/minimap2: remove redundanturirename

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/minimap2/minimap2-2.17.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild b/sci-biology/minimap2/minimap2-2.17.ebuild
index e40058243..e4f51e1d9 100644
--- a/sci-biology/minimap2/minimap2-2.17.ebuild
+++ b/sci-biology/minimap2/minimap2-2.17.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 DESCRIPTION="splice-aware sequence aligner"
 HOMEPAGE="https://github.com/lh3/minimap2"
-SRC_URI="https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17.tar.bz2 -> ${P}.tar.bz2"
+SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Martin Mokrejs]

commit:     6def45a03309ee5cee96b1b4988ab8c874d4f6df
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Tue Nov 30 11:54:26 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 30 11:54:26 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6def45a0

sci-biology/minimap2: version bump

Respect CFLAGS although the Makefile compiles different routines
for SSE4.1 processors. The options appear later on the commandline
so should override eventual CFLAGS -mtune and -march values.

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 .../minimap2/{minimap2-2.17.ebuild => minimap2-2.23.ebuild}        | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild b/sci-biology/minimap2/minimap2-2.23.ebuild
similarity index 76%
rename from sci-biology/minimap2/minimap2-2.17.ebuild
rename to sci-biology/minimap2/minimap2-2.23.ebuild
index e4f51e1d9..9f335e99c 100644
--- a/sci-biology/minimap2/minimap2-2.17.ebuild
+++ b/sci-biology/minimap2/minimap2-2.23.ebuild
@@ -3,6 +3,8 @@
 
 EAPI=7
 
+inherit toolchain-funcs
+
 DESCRIPTION="splice-aware sequence aligner"
 HOMEPAGE="https://github.com/lh3/minimap2"
 SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
@@ -15,6 +17,11 @@ DEPEND=""
 RDEPEND="${DEPEND}"
 BDEPEND=""
 
+src_prepare(){
+	sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
+	eapply_user
+}
+
 src_install(){
 	dobin "${PN}"
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Martin Mokrejs]

commit:     227e281f30db2fd020beda0f962166b4783c5d95
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Tue Nov 30 12:41:07 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 30 12:41:07 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=227e281f

sci-biology/minimap2: install more files, document incompleteness

I added notes on supported CPU instructions and additional python
bindings. Note the static library is linked into the minimap2 binary
by default but I think it may be handy to install the library and header
file too.

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/minimap2/minimap2-2.23.ebuild | 36 +++++++++++++++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/sci-biology/minimap2/minimap2-2.23.ebuild b/sci-biology/minimap2/minimap2-2.23.ebuild
index 9f335e99c..ed458b91d 100644
--- a/sci-biology/minimap2/minimap2-2.23.ebuild
+++ b/sci-biology/minimap2/minimap2-2.23.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 inherit toolchain-funcs
 
-DESCRIPTION="splice-aware sequence aligner"
+DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
 HOMEPAGE="https://github.com/lh3/minimap2"
 SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
 
@@ -13,7 +13,9 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
+IUSE="+static"
+
+DEPEND="sys-libs/zlib"
 RDEPEND="${DEPEND}"
 BDEPEND=""
 
@@ -22,6 +24,36 @@ src_prepare(){
 	eapply_user
 }
 
+# Minimap2 requires SSE2 instructions on x86 CPUs or NEON on ARM CPUs. It is
+# possible to add non-SIMD support, but it would make minimap2 slower by
+# several times.
+#
+# If you see compilation errors, try `make sse2only=1`
+# to disable SSE4 code, which will make minimap2 slightly slower.
+#
+# Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
+# compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To
+# compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1
+# aarch64=1`.
+#
+# Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
+# implementation to the different SIMD instruction sets. To compile using SIMDe,
+# use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
+# with the ARM related command lines given above.
+
+# This repository also provides Python bindings to a subset of C APIs. File
+# [python/README.rst](python/README.rst) gives the full documentation;
+# [python/minimap2.py](python/minimap2.py) shows an example. This Python
+# extension, mappy, is also [available from PyPI][mappypypi] via `pip install
+# mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
+
 src_install(){
 	dobin "${PN}"
+	insinto /usr/include
+	doins minimap.h mmpriv.h
+	dolib.a libminimap2.a
+	insinto /usr/share/"${PN}"/examples
+	doins example.c
+	doman minimap2.1
+	dodoc README.md NEWS.md FAQ.md
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Andrew Ammerlaan]

commit:     19fb6fba9514187c9c16052b5f93866d53858b55
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 13:05:12 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 13:05:12 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=19fb6fba

sci-biology/minimap2: version bump 2.24, add python flag

Closes: https://github.com/gentoo/sci/issues/1125
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/minimap2/minimap2-2.23.ebuild | 57 ----------------------------
 sci-biology/minimap2/minimap2-2.24.ebuild | 63 +++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 57 deletions(-)

diff --git a/sci-biology/minimap2/minimap2-2.23.ebuild b/sci-biology/minimap2/minimap2-2.23.ebuild
deleted file mode 100644
index eb8d98991..000000000
--- a/sci-biology/minimap2/minimap2-2.23.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
-HOMEPAGE="https://github.com/lh3/minimap2"
-SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="+static"
-
-DEPEND="sys-libs/zlib"
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-src_prepare(){
-	sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
-	eapply_user
-}
-
-# Minimap2 requires SSE2 instructions on x86 CPUs or NEON on ARM CPUs. It is
-# possible to add non-SIMD support, but it would make minimap2 slower by
-# several times.
-#
-# If you see compilation errors, try `make sse2only=1`
-# to disable SSE4 code, which will make minimap2 slightly slower.
-#
-# Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
-# compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To
-# compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1
-# aarch64=1`.
-#
-# Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
-# implementation to the different SIMD instruction sets. To compile using SIMDe,
-# use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
-# with the ARM related command lines given above.
-
-# This repository also provides Python bindings to a subset of C APIs. File
-# [python/README.rst](python/README.rst) gives the full documentation;
-# [python/minimap2.py](python/minimap2.py) shows an example. This Python
-# extension, mappy, is also [available from PyPI][mappypypi] via `pip install
-# mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
-
-src_install(){
-	dobin "${PN}"
-	insinto /usr/include
-	doins minimap.h mmpriv.h
-	dolib.a libminimap2.a
-	insinto /usr/share/"${PN}"/examples
-	doins example.c
-	doman minimap2.1
-	dodoc README.md NEWS.md FAQ.md
-}

diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild
new file mode 100644
index 000000000..f39de8ead
--- /dev/null
+++ b/sci-biology/minimap2/minimap2-2.24.ebuild
@@ -0,0 +1,63 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_OPTIONAL=1
+inherit distutils-r1
+
+DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
+HOMEPAGE="https://github.com/lh3/minimap2"
+SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="python cpu_flags_x86_sse4_1"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="sys-libs/zlib
+	python? (
+		${PYTHON_DEPS}
+	)"
+RDEPEND="${DEPEND}"
+BDEPEND="python? ( dev-python/cython[${PYTHON_USEDEP}] )"
+
+src_prepare(){
+	sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
+	if ! use cpu_flags_x86_sse4_1; then
+		sed -i -e "/extra_compile_args.append('-msse4.1')/d" setup.py || die
+	fi
+	if use python; then
+		distutils-r1_src_prepare
+	fi
+	default
+}
+
+src_configure() {
+	if use python; then
+		distutils-r1_src_configure
+	fi
+	default
+}
+
+src_compile() {
+	if use python; then
+		distutils-r1_src_compile
+	fi
+	default
+}
+
+src_install() {
+	if use python; then
+		distutils-r1_src_install
+	fi
+	dobin "${PN}"
+	insinto /usr/include
+	doins minimap.h mmpriv.h
+	insinto /usr/share/"${PN}"/examples
+	doins example.c
+	doman minimap2.1
+	einstalldocs
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/

[Horea Christian]

commit:     bed38d563364c22bbc8282b756602f453bd79bc3
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Mar 22 20:14:46 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Mar 22 20:14:46 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bed38d56

sci-biology/minimap2: update upstream metadata

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/minimap2/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/minimap2/metadata.xml b/sci-biology/minimap2/metadata.xml
index c9e82c96a..604410dd8 100644
--- a/sci-biology/minimap2/metadata.xml
+++ b/sci-biology/minimap2/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="github">minimap2</remote-id>
+		<remote-id type="github">lh3/minimap2</remote-id>
 	</upstream>
 </pkgmetadata>