Port details on branch 2022Q3 |
- spoa C++ implementation of the partial order alignment (POA) algorithm
- 4.1.0 biology =0 4.1.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-01-19 09:28:06
- Last Update: 2024-04-12 04:05:12
- Commit Hash: b963681
- License: MIT
- WWW:
- https://github.com/rvaser/spoa
- Description:
- Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA)
algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to
generate consensus sequences. It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap),
and three gap modes: linear, affine and convex (piecewise affine). It also
supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high
latency shifts), SIMDe and dispatching.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/spoa/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/spoa
- pkg install spoa
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: spoa
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1693289273
SHA256 (rvaser-spoa-4.1.0_GH0.tar.gz) = 43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8
SIZE (rvaser-spoa-4.1.0_GH0.tar.gz) = 47814
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:
-
- bioparser>0 : biology/bioparser
- biosoup>0 : biology/biosoup
- cereal>0 : devel/cereal
- simde>0 : devel/simde
- cmake : devel/cmake-core
- ninja : devel/ninja
- Test dependencies:
-
- googletest>0 : devel/googletest
- Runtime dependencies:
-
- cereal>0 : devel/cereal
- Library dependencies:
-
- libcpu_features.so : devel/cpu_features
- There are no ports dependent upon this port
Configuration Options:
- No options to configure
- Options name:
- biology_spoa
- USES:
- cmake compiler:c++11-lang localbase:ldflags
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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