4 files changed, 62 insertions, 0 deletions
diff --git a/biology/minimap2/DESCR b/biology/minimap2/DESCR
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+++ b/biology/minimap2/DESCR
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+Minimap2 is a versatile sequence alignment program that aligns DNA or
+mRNA sequences against a large reference database. Typical use cases
+include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
+human genome; (2) finding overlaps between long reads with error rate
+up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore
+cDNA or Direct RNA reads against a reference genome; (4) aligning
+Illumina single- or paired-end reads; (5) assembly-to-assembly
+alignment; (6) full-genome alignment between two closely related
+species with divergence below ~15%.
+
+For ~10kb noisy reads sequences, minimap2 is tens of times faster than
+mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and
+GMAP. It is more accurate on simulated long reads and produces
+biologically meaningful alignment ready for downstream analyses. For
+>100bp Illumina short reads, minimap2 is three times as fast as
+BWA-MEM and Bowtie2, and as accurate on simulated data.  Detailed
+evaluations are available from the minimap2 paper
+(https://doi.org/10.1093/bioinformatics/bty191).
diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
new file mode 100644
index 00000000000..fd0b19dfb96
--- /dev/null
+++ b/biology/minimap2/Makefile
@@ -0,0 +1,29 @@
+# $NetBSD: Makefile,v 1.1 2021/05/26 18:49:20 brook Exp $
+
+GITHUB_PROJECT=	minimap2
+GITHUB_TAG=	refs/tags/v2.18
+DISTNAME=	v2.18
+PKGNAME=	${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users@NetBSD.org
+HOMEPAGE=	https://github.com/lh3/minimap2
+COMMENT=	Minimap2 python binding
+LICENSE=	mit
+
+WRKSRC=		${WRKDIR}/minimap2-2.18
+USE_TOOLS+=	gmake
+
+INSTALLATION_DIRS+=	share/examples/minimap2
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/share/examples/minimap2
+	${INSTALL_DATA} ${WRKSRC}/cookbook.md ${DESTDIR}${PREFIX}/share/examples/minimap2
+
+BUILDLINK_DEPENDS.py-cython+=	build
+BUILDLINK_API_DEPENDS.py-cython+=	${PYPKGPREFIX}-cython>=0.29.23
+.include "../../devel/py-cython/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/minimap2/PLIST b/biology/minimap2/PLIST
new file mode 100644
index 00000000000..8c68d6a6aa6
--- /dev/null
+++ b/biology/minimap2/PLIST
@@ -0,0 +1,9 @@
+@comment $NetBSD: PLIST,v 1.1 2021/05/26 18:49:20 brook Exp $
+bin/minimap2.py
+${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/PKG-INFO
+${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/SOURCES.txt
+${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/dependency_links.txt
+${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/top_level.txt
+${PYSITELIB}/mappy.so
+share/examples/minimap2/README.md
+share/examples/minimap2/cookbook.md
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
new file mode 100644
index 00000000000..82a6670aff3
--- /dev/null
+++ b/biology/minimap2/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2021/05/26 18:49:20 brook Exp $
+
+SHA1 (minimap2/v2.18.tar.gz) = 77a4a1f955f0f8aaab7553b0d1b3bf3c102ea086
+RMD160 (minimap2/v2.18.tar.gz) = 33ff96cbdf5c4bd98a543ab8be644c337060d496
+SHA512 (minimap2/v2.18.tar.gz) = b2521ec453b836330eb6dcf87969e6171e7c1d53cee2767e6a36a0c422a9fa14c83a085b75371343ae119d719829bfe26b5d9f0008ccad1ac0f51b391a984860
+Size (minimap2/v2.18.tar.gz) = 231187 bytes