| Port details |
- minimap2 Pairwise aligner for genomic and spliced nucleotide sequences
- 2.28_1 biology
 =2      2.28_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2019-04-24 18:04:07
- Last Update: 2024-07-20 19:55:08
- Commit Hash: f84c631
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/lh3/minimap2
- 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%
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- minimap2>0:biology/minimap2
- To install the port:
- cd /usr/ports/biology/minimap2/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/minimap2
- pkg install minimap2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: minimap2
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: i386 mips powerpc powerpcspe
- distinfo:
- TIMESTAMP = 1713393837
SHA256 (lh3-minimap2-v2.28_GH0.tar.gz) = 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278
SIZE (lh3-minimap2-v2.28_GH0.tar.gz) = 260341
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- simde>0 : devel/simde
- gmake>=4.4.1 : devel/gmake
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_minimap2
- USES:
- gmake localbase
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.28_1
20 Jul 2024 19:55:08
 |
Jason W. Bacon (jwb) |
biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
Upstream supports specific architectures, mainly 64-bit and ARM Neon |
2.28_1
28 May 2024 21:06:42
|
Jason W. Bacon (jwb) |
biology/minimap2: Unbreak build on aarch64
Remove unsupports -msse flags
Reported by: pkg-fallout |
2.28_1
17 Apr 2024 22:52:15
|
Jason W. Bacon (jwb) |
biology/minimap2: Fix man prefix
Missed in last update, done just before prefix/man was obsoleted |
2.28
10 Apr 2024 12:28:02
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.28
Fix --MD flag
Add experimental lr:hqae
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout |
2.27_1
22 Mar 2024 07:29:47
|
Yasuhiro Kimura (yasu) |
biology/minimap2: Move man page to share/man
Approved by: portmgr (blanket) |
2.27
13 Mar 2024 13:44:27
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.27
Several new features and a few bug fixes
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout |
2.25_1
02 Mar 2024 19:29:26
|
Nuno Teixeira (eduardo) |
biology/minimap2: Move man pages to share/man
Approved by: portmgr (blanket) |
2.25
29 Apr 2023 14:53:40
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.25
New feature to output sequences in secondary alignments
Several minor enhancements and fixes
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.24
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
2.24
31 Dec 2021 14:30:52
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.24
Fix chaining algorithm issue resulting in poorly aligned regions
Reported by: portscout |
2.23_1
03 Dec 2021 17:22:37
|
Jason W. Bacon (jwb) |
biology/minimap2: Unbreak on i386 by resotring -msse flags |
2.23
30 Nov 2021 16:29:13
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.23
Also switch to SIMDE Makefile to support non-x86 platforms
Changes: https://github.com/lh3/minimap2/releases/tag/v2.23
Reported by: portscout |
2.22
25 Oct 2021 12:58:29
|
Alexey Dokuchaev (danfe) |
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names. |
2.22
22 Aug 2021 17:46:37
|
Jason W. Bacon (jwb) |
biology/minimap2: Add pkg-plist to repo |
2.22
22 Aug 2021 14:15:06
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.22
Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22
Reported by: portscout |
2.20
29 May 2021 21:06:34
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.20
Add "extra" binaries to install
Changes: https://github.com/lh3/minimap2/releases/tag/v2.20 |
2.18
11 Apr 2021 19:18:02
|
Jason W. Bacon (jwb) |
biology/minimap2: Update to 2.18
Numerous bug fixes and a few minor improvements
Reported by: portscout |
2.17
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.17
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.17
05 May 2019 14:56:07
 |
jwb |
biology/minimap2: Upgrade to 2.17
Reported by: portscout |
2.16
24 Apr 2019 18:03:49
|
jwb |
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database. |
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