diff options
-rw-r--r-- | biology/minimap2/DESCR | 18 | ||||
-rw-r--r-- | biology/minimap2/Makefile | 29 | ||||
-rw-r--r-- | biology/minimap2/PLIST | 9 | ||||
-rw-r--r-- | biology/minimap2/distinfo | 6 |
4 files changed, 62 insertions, 0 deletions
diff --git a/biology/minimap2/DESCR b/biology/minimap2/DESCR new file mode 100644 index 00000000000..97ba6a1796c --- /dev/null +++ b/biology/minimap2/DESCR @@ -0,0 +1,18 @@ +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 |