BSD Portsbiology/spoa 4.1.5 FreeBSD
C++ implementation of the partial order alignment (POA) algorithm
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- MIT
- Categories
- biology
- Package size
- 73.6 KiB, 192.7 KiB installed
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/spoa | 4.1.5 |
| DragonFly | biology/spoa | 4.1.0 |
| HardenedBSD | biology/spoa | 4.1.5 |
| GhostBSD | biology/spoa | 4.1.5 |
Install
Binary package:
pkg install spoaFrom the ports tree:
cd /usr/ports/biology/spoa/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= spoa>0:biology/spoa
LIB_DEPENDS= libspoa.so:biology/spoaPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 4.1.5 | 4.1.5 | - | - | - |
| FreeBSD:14:quarterly | 4.1.5 | 4.1.5 | n/a | - | - |
| FreeBSD:15:latest | 4.1.5 | 4.1.5 | n/a | - | - |
| FreeBSD:15:quarterly | 4.1.5 | 4.1.5 | n/a | n/a | n/a |
| FreeBSD:16:latest | 4.1.5 | 4.1.5 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 4
bioparser>0: biology/bioparserbiosoup>0: biology/biosoupcereal>0: devel/cerealsimde>0: devel/simde
Library 1
libcpu_features.so: devel/cpu_features
Runtime 1
cereal>0: devel/cereal
Test 1
googletest>0: devel/googletest
The full lists below include those, and their dependencies in turn.
Build dependencies 24
- archivers/liblz4
- archivers/zstd
- biology/bioparser
- biology/biosoup
- devel/boost-libs
- devel/cereal
- devel/cmake-core
- devel/cpu_features
- devel/gettext-runtime
- devel/icu
- devel/jsoncpp
- devel/libffi
- devel/libunistring
- devel/libuv
- devel/ninja
- devel/readline
- devel/simde
- dns/libidn2
- lang/python312
- math/mpdecimal
- ports-mgmt/pkg
- print/indexinfo
- security/rhash
- textproc/expat2
Run dependencies 6
No port depends on this one.
Configuration
No options to configure.
- USES
- cmake compiler:c++11-lang localbase:ldflags
- Service scripts
- none
Files
pkg-plist 11
- bin/spoa
- include/spoa/alignment_engine.hpp
- include/spoa/graph.hpp
- include/spoa/spoa.hpp
- include/spoa/version.hpp
- lib/cmake/spoa/spoaConfig.cmake
- lib/cmake/spoa/spoaConfigVersion.cmake
- lib/cmake/spoa/spoaTargets-.cmake
- lib/cmake/spoa/spoaTargets.cmake
- lib/libspoa.so
- lib/libspoa.so.7.0.0
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| rvaser-spoa-4.1.5_GH0.tar.gz | 47513 | b5d323740b01255c55725e88db2548c666a05bc83b825c19cfac10586e21e7b3 |
Commit history 0
No commits in the history this site was built from.