| Port details |
- mashmap Fast approximate aligner for long DNA sequences
- 3.1.1 biology
 =0      3.1.1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2023-07-11 01:45:07
- Last Update: 2023-10-11 18:26:35
- Commit Hash: 62a1698
- 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.
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- 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 = 1692721405
SHA256 (marbl-MashMap-v3.1.1_GH0.tar.gz) = b5794b181f91637940baf0230e8ddc60228bea041dda4588b03d2f8bc908c072
SIZE (marbl-MashMap-v3.1.1_GH0.tar.gz) = 25919337
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
- 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-3.1.1:
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
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 5
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
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 |
Number of commits found: 5
|
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