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Port details on branch 2022Q2
spoa C++ implementation of the partial order alignment (POA) algorithm
4.1.0 biology on this many watch lists=0 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 4.1.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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.
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 (18 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/spoa-4.1.0/catalog.mk
  3. /usr/local/share/licenses/spoa-4.1.0/LICENSE
  4. /usr/local/share/licenses/spoa-4.1.0/MIT
  5. bin/spoa
  6. include/spoa/alignment_engine.hpp
  7. include/spoa/graph.hpp
  8. include/spoa/spoa.hpp
  9. include/spoa/version.hpp
  10. lib/cmake/spoa/spoaConfig.cmake
  11. lib/cmake/spoa/spoaConfigVersion.cmake
  12. lib/cmake/spoa/spoaTargets-release.cmake
  13. lib/cmake/spoa/spoaTargets.cmake
  14. lib/libspoa.so
  15. lib/libspoa.so.7.0.0
  16. @owner
  17. @group
  18. @mode
Collapse this list.
Dependency lines:
  • spoa>0:biology/spoa
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):
spoa
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-4.1.0--4.1.0---
FreeBSD:13:quarterly-4.1.0--4.1.0---
FreeBSD:14:latest-4.1.0------
FreeBSD:14:quarterly-4.1.0------
FreeBSD:15:latest-4.1.0n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bioparser>0 : biology/bioparser
  2. biosoup>0 : biology/biosoup
  3. cereal>0 : devel/cereal
  4. simde>0 : devel/simde
  5. cmake : devel/cmake-core
  6. ninja : devel/ninja
Test dependencies:
  1. googletest>0 : devel/googletest
Runtime dependencies:
  1. cereal>0 : devel/cereal
Library dependencies:
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/rvaser/spoa/tar.gz/4.1.0?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port
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