BSD Portsbiology/minimap2 2.31 FreeBSD
Pairwise aligner for genomic and spliced nucleotide sequences
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology
- Package size
- 135.4 KiB, 439.8 KiB installed
Description
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 readsagainst 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%
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/minimap2 | 2.31 |
| NetBSD | biology/minimap2 | 2.28nb1 |
| DragonFly | biology/minimap2 | 2.28_1 |
| HardenedBSD | biology/minimap2 | 2.31 |
| GhostBSD | biology/minimap2 | 2.31 |
Install
Binary package:
pkg install minimap2From the ports tree:
cd /usr/ports/biology/minimap2/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= minimap2>0:biology/minimap2Packages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.31 | 2.31 | 2.24 | 2.30 | - |
| FreeBSD:14:quarterly | 2.31 | 2.31 | n/a | 2.30 | - |
| FreeBSD:15:latest | 2.31 | 2.31 | n/a | 2.30 | - |
| FreeBSD:15:quarterly | 2.31 | 2.31 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.31 | 2.31 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 1
simde>0: devel/simde
The full lists below include those, and their dependencies in turn.
Build dependencies 4
Required by 1
Configuration
No options to configure.
- USES
- gmake localbase
- Service scripts
- none
Files
Manual pages 1
- minimap2(1)
pkg-plist 13
- bin/minimap2
- bin/minimap2-lite
- bin/sdust
- share/man/man1/minimap2.1.gz
- share/minimap2/test/MT-human.fa
- share/minimap2/test/MT-orang.fa
- share/minimap2/test/q-inv.fa
- share/minimap2/test/q2.fa
- share/minimap2/test/t-inv.fa
- share/minimap2/test/t2.fa
- share/minimap2/test/x3s-aln.txt
- share/minimap2/test/x3s-qry.fa
- share/minimap2/test/x3s-ref.fa
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| lh3-minimap2-v2.31_GH0.tar.gz | 271153 | bff334a0e4512644e2f3e29944aeec408f49450f4f74dc39fe89e5273869255b |