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Port details on branch 2022Q3
py-pysam Python module for reading, manipulating and writing genomic data sets
0.19.1_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.19.1_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-08-14 00:04:10
Last Update: 2022-07-19 15:53:29
Commit Hash: 38c74de
Also Listed In: python
License: MIT
WWW:
https://github.com/pysam-developers/pysam
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. WWW: https://github.com/pysam-developers/pysam
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR}
To install the port:
cd /usr/ports/biology/py-pysam/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-pysam
  • pkg install py39-pysam
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-pysam listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-pysam
Package flavors (<flavor>: <package>)
  • py39: py39-pysam
distinfo:
TIMESTAMP = 1658245018 SHA256 (pysam-0.19.1.tar.gz) = dee403cbdf232170c1e11cc24c76e7dd748fc672ad38eb0414f3b9d569b1448f SIZE (pysam-0.19.1.tar.gz) = 3857553

Expand this list (2 items)

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SHA256 (064c8024395a15024fd590bd90f55f918e15545f.patch) = e4655d70d0debe00f7937b9b3f18318acbcb8ae832165542c1531233320c6df7 SIZE (064c8024395a15024fd590bd90f55f918e15545f.patch) = 1237

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No package information for this port in our database
Sometimes this happens. Not all ports have packages.
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. cython-3.9 : lang/cython@py39
  3. py39-setuptools>=62.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Runtime dependencies:
  1. cython-3.9 : lang/cython@py39
  2. py39-setuptools>=62.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_py-pysam
USES:
gmake python:3.6-3.9
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
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  1. https://files.pythonhosted.org/packages/source/p/pysam/
  2. https://pypi.org/packages/source/p/pysam/
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Number of commits found: 4

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.19.1_1
19 Jul 2022 15:53:29
commit hash: 38c74de9d54d2f98cf1245941e2bd5453156d01bcommit hash: 38c74de9d54d2f98cf1245941e2bd5453156d01bcommit hash: 38c74de9d54d2f98cf1245941e2bd5453156d01bcommit hash: 38c74de9d54d2f98cf1245941e2bd5453156d01b files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pysam: Remove BROKEN lines

(cherry picked from commit 978fbbf602c743b555117a6c25a836ebfa5bbaf2)
0.19.1_1
19 Jul 2022 15:53:29
commit hash: 09ae0e0b7bf4132bfe44ae04e0bb416d6bf004c3commit hash: 09ae0e0b7bf4132bfe44ae04e0bb416d6bf004c3commit hash: 09ae0e0b7bf4132bfe44ae04e0bb416d6bf004c3commit hash: 09ae0e0b7bf4132bfe44ae04e0bb416d6bf004c3 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix

(cherry picked from commit 8e9198d4043c9022df3502499e3deb1e988d2b9e)
0.19.1
19 Jul 2022 02:11:05
commit hash: b6c69cd6ff00ebc94951db5ea2c77186d07c7ed4commit hash: b6c69cd6ff00ebc94951db5ea2c77186d07c7ed4commit hash: b6c69cd6ff00ebc94951db5ea2c77186d07c7ed4commit hash: b6c69cd6ff00ebc94951db5ea2c77186d07c7ed4 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pysam: Correct BROKEN line; Add comment

(cherry picked from commit 09d9d827a5c165377dc9e225241b248ea7d145c8)
0.19.1
19 Jul 2022 02:11:04
commit hash: f2be3d383cd58fcd9eb21919669d000bb2c177abcommit hash: f2be3d383cd58fcd9eb21919669d000bb2c177abcommit hash: f2be3d383cd58fcd9eb21919669d000bb2c177abcommit hash: f2be3d383cd58fcd9eb21919669d000bb2c177ab files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pysam: Broken on arm64 and riscv64

Reported by:	fallout

(cherry picked from commit 2f374bcdfe524d910349e06d52bde62047650b41)

Number of commits found: 4