BSD Portsbiology/py-pysam 0.24.1 FreeBSD
Python module for reading, manipulating and writing genomic data sets
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
d1cc54b504- License
- MIT
- Categories
- biology, python
- Package size
- 1561.3 KiB, 5411.1 KiB installed
Description
pysam is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.
This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/py-pysam | 0.24.1 |
| DragonFly | biology/py-pysam | 0.23.0_1 |
| HardenedBSD | biology/py-pysam | 0.24.1 |
| GhostBSD | biology/py-pysam | 0.24.1 |
Install
Binary package:
pkg install py312-pysamFrom the ports tree:
cd /usr/ports/biology/py-pysam/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= py312-pysam>0:biology/py-pysamPackages
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 | 0.24.1 | 0.24.1 | 0.20.0 | - | 0.24.1 |
| FreeBSD:14:quarterly | 0.24.1 | 0.24.1 | n/a | - | 0.24.1 |
| FreeBSD:15:latest | 0.24.1 | 0.24.1 | n/a | - | 0.23.0_1 |
| FreeBSD:15:quarterly | 0.24.1 | 0.24.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 0.24.1 | 0.24.1 | 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.
Library 1
libhts.so: biology/htslib
Runtime 2
bcftools: biology/bcftoolssamtools: biology/samtools
The full lists below include those, and their dependencies in turn.
Build dependencies 22
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/htslib
- devel/gettext-runtime
- devel/gmake
- devel/libffi
- devel/libunistring
- devel/py-setuptools
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/cython
- lang/python312
- lang/python315
- math/mpdecimal
- print/indexinfo
- security/libssh2
- textproc/expat2
- www/libnghttp2
Run dependencies 25
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/bcftools
- biology/htslib
- biology/samtools
- devel/gettext-runtime
- devel/libffi
- devel/libunistring
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/cython
- lang/perl5.42
- lang/python312
- lang/python315
- math/gsl
- math/mpdecimal
- print/indexinfo
- security/libssh2
- shells/bash
- textproc/expat2
- www/libnghttp2
Configuration
No options to configure.
- USES
- gmake python
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| pysam-developers-pysam-v0.24.1_GH0.tar.gz | 4.2306e+06 | 78d65401f5dac1533167b20e8f697572a4aac5471fdca2abc699c6c8a101215b |