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freebsd-ports/biology/py-pysam/Makefile

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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. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:05:24 +02:00
PORTNAME= pysam
biology/py-pysam: Update 0.19.0 -> 0.19.1 Reported by: portscout
2022-05-31 01:15:56 +02:00
DISTVERSION= 0.19.1
biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix
2022-07-19 17:45:31 +02:00
PORTREVISION= 1
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. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:05:24 +02:00
CATEGORIES= biology python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix
2022-07-19 17:45:31 +02:00
PATCH_SITES= https://github.com/pysam-developers/pysam/commit/
PATCHFILES= 064c8024395a15024fd590bd90f55f918e15545f.patch:-p1 # backport of symbols failure fix for arm and risc
biology/py-pysam: Update to 0.13 Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D12967
2017-11-05 20:12:28 +01:00
MAINTAINER= yuri@FreeBSD.org
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. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:05:24 +02:00
COMMENT= Python module for reading, manipulating and writing genomic data sets
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/COPYING
biology/py-pysam: limit supported python versions pysam/libchtslib.c:1269:15: error: no member named 'use_tracing' in 'struct _ts' tstate->use_tracing = 0; Approved by: portmgr blanket
2021-10-28 16:53:53 +02:00
USES= gmake python:3.6-3.9
Convert Python ports to FLAVORS. Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464
2017-11-30 16:50:30 +01:00
USE_PYTHON= autoplist distutils cython cython_run
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. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:05:24 +02:00
.include <bsd.port.mk>
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