| Port details |
- seqwish Alignment to variation graph inducer
- 0.7.9 biology
 =0      0.7.9Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2023-07-21 21:42:05
- Last Update: 2023-11-05 23:07:52
- Commit Hash: 25d04c6
- License: MIT
- WWW:
- https://github.com/ekg/seqwish
- Description:
- seqwish implements a lossless conversion from pairwise alignments between
sequences to a variation graph encoding the sequences and their alignments.
As input we typically take all-versus-all alignments, but the exact structure
of the alignment set may be defined in an application specific way. This
algorithm uses a series of disk-backed sorts and passes over the alignment and
sequence inputs to allow the graph to be constructed from very large inputs
that are commonly encountered when working with large numbers of noisy input
sequences. Memory usage during construction and traversal is limited by the use
of sorted disk-backed arrays and succinct rank/select dictionaries to record a
queryable version of the graph.
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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:
-
- seqwish>0:biology/seqwish
- To install the port:
- cd /usr/ports/biology/seqwish/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/seqwish
- pkg install seqwish
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: seqwish
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1689972439
SHA256 (seqwish-v0.7.9.tar.gz) = 1ca7ebf02a35ad147c8a2b81f087aaba2deb878fec7acb4deb9f14e932e89d36
SIZE (seqwish-v0.7.9.tar.gz) = 12116251
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
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for seqwish-0.7.9:
OPENMP=on: Parallel processing support via OpenMP
===> Use 'make config' to modify these settings
- Options name:
- biology_seqwish
- USES:
- cmake:noninja
- 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 |
|---|
0.7.9
05 Nov 2023 23:07:52
 |
Yuri Victorovich (yuri) |
biology/seqwish: Add comment |
0.7.9
25 Aug 2023 06:22:32
|
Yuri Victorovich (yuri) |
biology/seqwish: Add comment |
0.7.9
17 Aug 2023 05:27:09
|
Yuri Victorovich (yuri) |
biology/seqwish: Broken on i386
Reported by: fallout |
0.7.9
21 Jul 2023 23:47:03
|
Yuri Victorovich (yuri) |
biology/seqwish: Correct COMMENT and WWW |
0.7.9
21 Jul 2023 21:38:59
|
Yuri Victorovich (yuri) |
biology/seqwish: New port: Assembly By Short Sequences: parallel, paired-end
sequence assembler |
Number of commits found: 5
|
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