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Port details
minimap2 Pairwise aligner for genomic and spliced nucleotide sequences
2.28_1 biology on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.28_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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%
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (16 items)
Collapse this list.
  1. /usr/local/share/licenses/minimap2-2.28_1/catalog.mk
  2. /usr/local/share/licenses/minimap2-2.28_1/LICENSE
  3. /usr/local/share/licenses/minimap2-2.28_1/MIT
  4. bin/minimap2
  5. bin/minimap2-lite
  6. bin/sdust
  7. share/man/man1/minimap2.1.gz
  8. share/minimap2/test/MT-human.fa
  9. share/minimap2/test/MT-orang.fa
  10. share/minimap2/test/q-inv.fa
  11. share/minimap2/test/q2.fa
  12. share/minimap2/test/t-inv.fa
  13. share/minimap2/test/t2.fa
  14. @owner
  15. @group
  16. @mode
Collapse this list.
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):
minimap2
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.28_12.28_1-2.28_1----
FreeBSD:13:quarterly2.28_12.28_12.252.28_1-2.252.252.25
FreeBSD:14:latest2.28_12.28_12.242.28_1-2.25-2.25
FreeBSD:14:quarterly2.28_12.28_1-2.28_1-2.252.252.25
FreeBSD:15:latest2.28_12.28_1n/a2.28_1n/a2.252.252.25
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. simde>0 : devel/simde
  2. gmake>=4.4.1 : devel/gmake
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/lh3/minimap2/tar.gz/v2.28?dummy=/
Collapse this list.

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.28_1
20 Jul 2024 19:55:08
commit hash: f84c63104e8cde852cffab5b4702d8e5fb70a2c2commit hash: f84c63104e8cde852cffab5b4702d8e5fb70a2c2commit hash: f84c63104e8cde852cffab5b4702d8e5fb70a2c2commit hash: f84c63104e8cde852cffab5b4702d8e5fb70a2c2 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 859980f9d8c367755a0f363f7de68d9c62758c6ecommit hash: 859980f9d8c367755a0f363f7de68d9c62758c6ecommit hash: 859980f9d8c367755a0f363f7de68d9c62758c6ecommit hash: 859980f9d8c367755a0f363f7de68d9c62758c6e files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/minimap2: Unbreak build on aarch64

Remove unsupports -msse flags

Reported by:    pkg-fallout
2.28_1
17 Apr 2024 22:52:15
commit hash: 507fa8ab37097cb9718bf3aa5fe7ca4a6cc2ccf8commit hash: 507fa8ab37097cb9718bf3aa5fe7ca4a6cc2ccf8commit hash: 507fa8ab37097cb9718bf3aa5fe7ca4a6cc2ccf8commit hash: 507fa8ab37097cb9718bf3aa5fe7ca4a6cc2ccf8 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/minimap2: Fix man prefix

Missed in last update, done just before prefix/man was obsoleted
2.28
10 Apr 2024 12:28:02
commit hash: 8efa6a2283076e4e556d7796161c44b90f5b3aa8commit hash: 8efa6a2283076e4e556d7796161c44b90f5b3aa8commit hash: 8efa6a2283076e4e556d7796161c44b90f5b3aa8commit hash: 8efa6a2283076e4e556d7796161c44b90f5b3aa8 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: eb44cf3c6f2638afa81b13177c442ae96f58f236commit hash: eb44cf3c6f2638afa81b13177c442ae96f58f236commit hash: eb44cf3c6f2638afa81b13177c442ae96f58f236commit hash: eb44cf3c6f2638afa81b13177c442ae96f58f236 files touched by this commit		 Yasuhiro Kimura (yasu) search for other commits by this committer 
biology/minimap2: Move man page to share/man

Approved by:	portmgr (blanket)
2.27
13 Mar 2024 13:44:27
commit hash: 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848fcommit hash: 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848fcommit hash: 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848fcommit hash: 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848f files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: f246c253710829601f535edf81675b26f6b1755acommit hash: f246c253710829601f535edf81675b26f6b1755acommit hash: f246c253710829601f535edf81675b26f6b1755acommit hash: f246c253710829601f535edf81675b26f6b1755a files touched by this commit		 Nuno Teixeira (eduardo) search for other commits by this committer 
biology/minimap2: Move man pages to share/man

Approved by:	portmgr (blanket)
2.25
29 Apr 2023 14:53:40
commit hash: 57d280a35eb7d931d7009182b8dd2289c946f391commit hash: 57d280a35eb7d931d7009182b8dd2289c946f391commit hash: 57d280a35eb7d931d7009182b8dd2289c946f391commit hash: 57d280a35eb7d931d7009182b8dd2289c946f391 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
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 View all of this commit message)
2.24
31 Dec 2021 14:30:52
commit hash: 2b4cfc8ff39b9c6afa6984ca1deb5e0ce612608bcommit hash: 2b4cfc8ff39b9c6afa6984ca1deb5e0ce612608bcommit hash: 2b4cfc8ff39b9c6afa6984ca1deb5e0ce612608bcommit hash: 2b4cfc8ff39b9c6afa6984ca1deb5e0ce612608b files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 8261e82cd510324b14e5463928e537a342cbddbfcommit hash: 8261e82cd510324b14e5463928e537a342cbddbfcommit hash: 8261e82cd510324b14e5463928e537a342cbddbfcommit hash: 8261e82cd510324b14e5463928e537a342cbddbf files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/minimap2: Unbreak on i386 by resotring -msse flags
2.23
30 Nov 2021 16:29:13
commit hash: 325754dd3899cb5b179ebc6ef87fbe4f4648c6adcommit hash: 325754dd3899cb5b179ebc6ef87fbe4f4648c6adcommit hash: 325754dd3899cb5b179ebc6ef87fbe4f4648c6adcommit hash: 325754dd3899cb5b179ebc6ef87fbe4f4648c6ad files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 files touched by this commit		 Alexey Dokuchaev (danfe) search for other commits by this committer 
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
commit hash: d09fdd5d58f48741598964eea8e0ca227638d6dccommit hash: d09fdd5d58f48741598964eea8e0ca227638d6dccommit hash: d09fdd5d58f48741598964eea8e0ca227638d6dccommit hash: d09fdd5d58f48741598964eea8e0ca227638d6dc files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/minimap2: Add pkg-plist to repo
2.22
22 Aug 2021 14:15:06
commit hash: 205fcac2210ba735dde3e037616661ab16cd5e66commit hash: 205fcac2210ba735dde3e037616661ab16cd5e66commit hash: 205fcac2210ba735dde3e037616661ab16cd5e66commit hash: 205fcac2210ba735dde3e037616661ab16cd5e66 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: da0bb00a74646f1a22eed576fb041c0d04a03a19commit hash: da0bb00a74646f1a22eed576fb041c0d04a03a19commit hash: da0bb00a74646f1a22eed576fb041c0d04a03a19commit hash: da0bb00a74646f1a22eed576fb041c0d04a03a19 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: a2fa05009fd280fcf8e93f1062b554fdcca63c9acommit hash: a2fa05009fd280fcf8e93f1062b554fdcca63c9acommit hash: a2fa05009fd280fcf8e93f1062b554fdcca63c9acommit hash: a2fa05009fd280fcf8e93f1062b554fdcca63c9a files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.17
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
2.17
05 May 2019 14:56:07
Revision:500860Original commit files touched by this commit		 jwb search for other commits by this committer 
biology/minimap2: Upgrade to 2.17

Reported by:    portscout
2.16
24 Apr 2019 18:03:49
Revision:499895Original commit files touched by this commit		 jwb search for other commits by this committer 
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.

Number of commits found: 22
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