| Port details |
- wfa2-lib Exact gap-affine algorithm using homology to accelerate alignment
- 2.3.5 biology
 =2      2.3.5Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2023-01-30 19:12:07
- Last Update: 2024-08-04 12:00:47
- Commit Hash: a732098
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/smarco/WFA2-lib
- Description:
- The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process. Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- wfa2-lib>0:biology/wfa2-lib
- To install the port:
- cd /usr/ports/biology/wfa2-lib/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/wfa2-lib
- pkg install wfa2-lib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: wfa2-lib
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1713703314
SHA256 (smarco-WFA2-lib-v2.3.5_GH0.tar.gz) = 2609d5f267f4dd91dce1776385b5a24a2f1aa625ac844ce0c3571c69178afe6e
SIZE (smarco-WFA2-lib-v2.3.5_GH0.tar.gz) = 4225016
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
- ninja : devel/ninja
- pkgconf>=1.3.0_1 : devel/pkgconf
- This port is required by:
- for Libraries
-
- biology/vcflib
Configuration Options:- No options to configure
- Options name:
- biology_wfa2-lib
- USES:
- cmake pkgconfig
- 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 |
|---|
2.3.5
04 Aug 2024 12:00:47
 |
Piotr Kubaj (pkubaj) |
biology/wfa2-lib: fix build without libomp
/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c:32:10:
fatal error: 'omp.h' file not found
32 | #include <omp.h>
| ^~~~~~~
1 error generated. |
2.3.5
22 Apr 2024 12:42:04
|
Jason W. Bacon (jwb) |
biology/wfa2-lib: Update to 2.3.5
A few bug fixes.
Changes: https://github.com/smarco/WFA2-lib/releases
Reported by: portscout |
2.3.4
29 Sep 2023 18:24:07
|
Jason W. Bacon (jwb) |
biology/wfa2-lib: Update to 2.3.4
A few bug fixes
Changes: https://github.com/smarco/WFA2-lib/releases
Reported by: portscout |
2.3.2_1
30 Mar 2023 23:59:51
|
Muhammad Moinur Rahman (bofh) |
*/*: Sunset 12.3-RELEASE from ports tree
- Mk/bsd.port.mk: mark FreeBSD 12.3 as unsupported.
- Mk/Uses/cabal.mk: Remove the text-2 workaround for 12.3-RELEASE
- biology/wfa2-lib: remove obsolete patch
- databases/mongodb60: remove IGNORE for EOL FreeBSD 12.3
- devel/concurrencpp: remove workaround for EOL FreeBSD 12.3
- devel/electron22: remove IGNORE for EOL FreeBSD 12.3
- devel/malloy: this should build fine on 12.4-RELEASE
- devel/qcoro: remove BROKEN for EOL FreeBSD 12.3
- devel/root: remove workaround for EOL FreeBSD 12.3
- editors/imhex: remove IGNORE for EOL FreeBSD 12.3
- emulators/ppsspp: remove workaround for EOL FreeBSD 12.3
- emulators/rpcs3: remove workaround for EOL FreeBSD 12.3
- emulators/yuzu: remove workaround for EOL 12.3-RELEASE (Only the first 15 lines of the commit message are shown above  ) |
2.3.2_1
31 Jan 2023 15:17:52
|
Jason W. Bacon (jwb) |
biology/wfa2-lib: Unbreak build on aarch64, probably others
Patch out hard-coded -march=native, not supported by clang aarch64
Reported by: pkg-fallout |
2.3.2
30 Jan 2023 19:09:02
|
Jason W. Bacon (jwb) |
biology/wfa2-lib: Exact gap-affine algorithm using homology
The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process. Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code. |
As an Amazon Associate I earn from qualifying purchases.