textproc/py-affine-gaps 0.2.4
JIT-compiled string edit-distances
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Port added
- Last update
- Commit
2a722c0616- License
- APACHE20
- Categories
- textproc, python
- Package size
- 24.9 KiB, 153.1 KiB installed
Description
Affine Gaps is a single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman-Wunsch and Smith-Waterman algorithms used for global and local sequence alignment in bioinformatics.
It includes command-line and Python interfaces for computing optimal alignments and alignment scores.
Install
As a binary package — by origin, or by package name:
pkg install textproc/py-affine-gaps
pkg install py312-affine-gapsFrom the ports tree:
cd /usr/ports/textproc/py-affine-gaps/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= py312-affine-gaps>0:textproc/py-affine-gapsPackages
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 | 0.2.4 | 0.2.4 | - | - | 0.2.4 |
| FreeBSD:14:quarterly | 0.2.4 | 0.2.4 | n/a | - | 0.2.4 |
| FreeBSD:15:latest | 0.2.4 | 0.2.4 | n/a | - | - |
| FreeBSD:15:quarterly | 0.2.4 | 0.2.4 | n/a | n/a | n/a |
| FreeBSD:16:latest | 0.2.4 | 0.2.4 | 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 1
${PYTHON_PKGNAMEPREFIX}hatchling>0: devel/py-hatchling
Runtime 3
${PYTHON_PKGNAMEPREFIX}numpy>0: math/py-numpy${PYTHON_PKGNAMEPREFIX}colorama>0: devel/py-colorama${PYTHON_PKGNAMEPREFIX}numba>0: devel/py-numba
Test 3
${PYTHON_PKGNAMEPREFIX}biopython>0: biology/py-biopython${PYTHON_PKGNAMEPREFIX}pytest-repeat>0: devel/py-pytest-repeat${PYTHON_PKGNAMEPREFIX}stringzilla>0: devel/py-stringzilla
The full lists below include those, and their dependencies in turn.
All build dependencies 19
- archivers/liblz4
- archivers/zstd
- devel/gettext-runtime
- devel/libffi
- devel/py-build
- devel/py-hatchling
- devel/py-installer
- devel/py-packaging
- devel/py-pathspec
- devel/py-pluggy
- devel/py-pyproject-hooks
- devel/py-trove-classifiers
- devel/readline
- lang/python312
- lang/python315
- math/mpdecimal
- print/indexinfo
- textproc/expat2
- textproc/py-tomlkit
All run dependencies 26
- archivers/liblz4
- archivers/zstd
- devel/binutils
- devel/gettext-runtime
- devel/hwloc2
- devel/level-zero
- devel/libffi
- devel/libpciaccess
- devel/llvm22
- devel/onetbb
- devel/py-colorama
- devel/py-llvmlite
- devel/py-numba
- devel/readline
- lang/gcc14
- lang/python312
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-numpy
- misc/hwdata
- print/indexinfo
- textproc/expat2
- textproc/libxml2
No port depends on this one.
Configuration
No options to configure.
- USES
- python
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| affine_gaps-0.2.4.tar.gz | 22505 | 2c85685fc82f3c8a610522e07e56e031f3f2985ab96f5b708ebf8db8cf342de8 |
Master sites 1
- PYPI
Commit history 1
| Date | Commit | Credits | Log message |
|---|---|---|---|
2a722c0616 |
Yuri Victorovich | textproc/py-affine-gaps: New port: JIT-compiled string edit-distances PR: 298330
Approved by: Baptiste Daroussin <[email protected]> (on behalf of portmgr@) |