| Port details |
- mashmap Fast approximate aligner for long DNA sequences
- 3.1.3 biology
 =2      3.1.3Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2023-07-11 01:45:07
- Last Update: 2024-01-13 01:57:41
- Commit Hash: f98bd5d
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: PD
- WWW:
- https://github.com/marbl/MashMap
- Description:
- MashMap implements a fast and approximate algorithm for computing local
alignment boundaries between long DNA sequences. It can be useful for mapping
genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a
minimum alignment length and an identity threshold for the desired local
alignments, Mashmap computes alignment boundaries and identity estimates using
k-mers. It does not compute the alignments explicitly, but rather estimates an
unbiased k-mer based Jaccard similarity using a combination of minmers (a novel
winnowing scheme) and MinHash. This is then converted to an estimate of sequence
identity using the Mash distance. An appropriate k-mer sampling rate is
automatically determined using the given minimum local alignment length and
identity thresholds.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- mashmap>0:biology/mashmap
- To install the port:
- cd /usr/ports/biology/mashmap/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/mashmap
- pkg install mashmap
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: mashmap
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1704429274
SHA256 (marbl-MashMap-v3.1.3_GH0.tar.gz) = 7719dd6b3c25e650e16218252eaae7dbf424a10890d717ec3ad0920b102fd05a
SIZE (marbl-MashMap-v3.1.3_GH0.tar.gz) = 25919699
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:
-
- cmake : devel/cmake-core
- ninja : devel/ninja
- pkgconf>=1.3.0_1 : devel/pkgconf
- Library dependencies:
-
- libgsl.so : math/gsl
- libhts.so : biology/htslib
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for mashmap-3.1.3:
NATIVE=off: Use native optimization (-march=native)
===> Use 'make config' to modify these settings
- Options name:
- biology_mashmap
- USES:
- cmake compiler:c++17-lang localbase:ldflags pkgconfig
- 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 |
|---|
3.1.3
13 Jan 2024 01:57:41
 |
Yuri Victorovich (yuri) |
biology/mashmap: Broken on armv7
Reported by: https://portsfallout.com/ |
3.1.3
05 Jan 2024 09:38:15
|
Yuri Victorovich (yuri) |
biology/mashmap: update 3.1.2 → 3.1.3 |
3.1.2
06 Dec 2023 08:34:56
|
Yuri Victorovich (yuri) |
biology/mashmap: update 3.1.1 → 3.1.2
Reported by: portscout |
3.1.1
11 Oct 2023 18:26:35
|
Piotr Kubaj (pkubaj) |
biology/mashmap: disable on powerpc |
3.1.1
22 Aug 2023 16:32:45
|
Yuri Victorovich (yuri) |
biology/mashmap: Update 3.1.0 → 3.1.1 |
3.1.0
22 Aug 2023 06:55:32
|
Yuri Victorovich (yuri) |
biology/mashmap: Update 3.0.6 → 3.1.0
Reported by: portscout |
3.0.6_1
19 Jul 2023 18:26:06
|
Yuri Victorovich (yuri) |
biology/mashmap: Broken on i386; Fix build on other architectures by using
NATIVE option
Reported by: fallout |
3.0.6
11 Jul 2023 01:44:34
|
Yuri Victorovich (yuri) |
biology/mashmap: New port: Fast approximate aligner for long DNA sequences |
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