| Port details |
- spoa C++ implementation of the partial order alignment (POA) algorithm
- 4.1.0 biology
 =2      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
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
4.1.0
12 Apr 2024 04:05:12
 |
Yuri Victorovich (yuri) |
biology/spoa: Broken on i386
Reported by: fallout |
4.1.0
29 Aug 2023 16:59:01
|
Yuri Victorovich (yuri) |
biology/spoa: update 4.0.7 → 4.1.0
Reported by: portscout |
4.0.7_4
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
4.0.7_3
12 Aug 2022 14:46:53
|
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
4.0.7_2
26 Jan 2022 16:45:29
|
Yuri Victorovich (yuri) |
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
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
4.0.7_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
4.0.7_2
04 Mar 2021 19:18:54
 |
pkubaj |
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
|
yuri |
biology/spoa: Fix build after recent devel/cereal update; Fix LIB_DEPENDS
Reported by: fallout |
4.0.7
19 Jan 2021 09:28:01
|
yuri |
New port: biology/spoa: C++ implementation of the partial order alignment (POA)
algorithm |
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