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Port details
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: 2023-08-29 16:59:01
Commit Hash: e06be01
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--4.1.0---
FreeBSD:14:quarterly-4.1.0--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.

Number of commits found: 11

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.1.0
29 Aug 2023 16:59:01
commit hash: e06be01f1ef131f645cf2177b38758acf7a2e48acommit hash: e06be01f1ef131f645cf2177b38758acf7a2e48acommit hash: e06be01f1ef131f645cf2177b38758acf7a2e48acommit hash: e06be01f1ef131f645cf2177b38758acf7a2e48a files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/spoa: update 4.0.7 → 4.1.0

Reported by:	portscout
4.0.7_4
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
4.0.7_3
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.0.7_3
12 Aug 2022 14:46:53
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
4.0.7_2
26 Jan 2022 16:45:29
commit hash: d709ba8de8ec14887beffe99233eec09b26b7ed1commit hash: d709ba8de8ec14887beffe99233eec09b26b7ed1commit hash: d709ba8de8ec14887beffe99233eec09b26b7ed1commit hash: d709ba8de8ec14887beffe99233eec09b26b7ed1 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
devel/cpu_features: Install cmake files, install headers into a dedicated
directory

do-install is removed in favor of project's install target,

Also update 3 other ports to build with cpu_features.

PR:		261252
Approved by:	skreuzer@ (maintainer)
4.0.7_2
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
4.0.7_2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
4.0.7_2
04 Mar 2021 19:18:54
Revision:567333Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/spoa: fix build on non-x86

In file included from
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp:7:
/usr/local/include/cpuinfo_x86.h:228:2: error: "Including cpuinfo_x86.h from a
non-x86 target."
#error "Including cpuinfo_x86.h from a non-x86 target."
4.0.7_2
19 Feb 2021 09:22:30
Revision:566037Original commit files touched by this commit
yuri search for other commits by this committer
biology/spoa: Fix build after recent devel/cereal update; Fix LIB_DEPENDS

Reported by:	fallout
4.0.7
19 Jan 2021 09:28:01
Revision:562036Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/spoa: C++ implementation of the partial order alignment (POA)
algorithm

Number of commits found: 11