[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
 }