biology/py-macs3 3.0.5 FreeBSD

Peak caller aimed at transcription factor binding sites

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-08
Commit: 2414383046
License: BSD3CLAUSE
Categories: biology, python

Description

MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin.

In the other systems

The newest version among them is 3.0.5, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/py-macs3

3.0.5 newest

none known

[email protected]

2026-10-08

NetBSD

biology/py-macs3

3.0.2nb2 behind since 2026-09-26

none known

[email protected]

2026-10-16

DragonFly

biology/py-macs3

3.0.3 behind since 2026-09-26

none known

[email protected]

HardenedBSD

biology/py-macs3

3.0.5 newest

no data

[email protected]

GhostBSD

biology/py-macs3

3.0.4_1 behind since 2026-09-26

no data

[email protected]

Compare across BSDs

Version history 1

3.0.5 2026-09-26 8cd5ea075a

Upstream's version as each commit to the port's Makefile set it, or as this site first saw it in the system's packages; the tree's own revisions are not versions here.

Install

Binary package:

pkg install py312-MACS3

From the ports tree:

cd /usr/ports/biology/py-macs3/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	py312-MACS3>0:biology/py-macs3

Packages

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	-	3.0.5	-	3.0.3	-
FreeBSD:14:quarterly	-	3.0.5	n/a	3.0.3	-
FreeBSD:15:latest	-	3.0.5	n/a	3.0.3	-
FreeBSD:15:quarterly	-	3.0.5	n/a	n/a	n/a
FreeBSD:16:latest	-	3.0.5	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/py-macs3"]
  u0["biology/atac-seq"] --> me
  u1["biology/chip-seq"] --> me
  me --> d0["archivers/liblz4"]
  me --> d1["archivers/zstd"]
  me --> d2["devel/binutils"]
  me --> d3["devel/gettext-runtime"]
  me --> d4["devel/libffi"]
  me --> d5["devel/py-cloudpickle"]
  me --> d6["devel/py-cykhash"]
  me --> d7["devel/py-joblib"]
  me -.-> dmore(["17 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Build 7

${PYTHON_PKGNAMEPREFIX}wheel>0 : devel/py-wheel
${PYTHON_PKGNAMEPREFIX}setuptools>=0 : devel/py-setuptools
simde>0 : devel/simde
${PYTHON_PKGNAMEPREFIX}scipy>1.11.1 : science/py-scipy
${PYTHON_PKGNAMEPREFIX}cykhash>=2.0,<3.0 : devel/py-cykhash
${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.3 : science/py-scikit-learn
${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2 : math/py-hmmlearn

Runtime 4

${PYTHON_PKGNAMEPREFIX}scipy>1.11.1 : science/py-scipy
${PYTHON_PKGNAMEPREFIX}cykhash>=2.0,<3.0 : devel/py-cykhash
${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.3 : science/py-scikit-learn
${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2 : math/py-hmmlearn

Test 2

${PYTHON_PKGNAMEPREFIX}pytest>0 : devel/py-pytest
bash : shells/bash

The full lists below include those, and their dependencies in turn.

Build dependencies 34

Run dependencies 25

Required by 2

Configuration

No options to configure.

USES: localbase perl5 python shebangfix
Service scripts: none

Files

distinfo 1

File

Size

SHA256

macs3-project-MACS-v3.0.5_GH0.tar.gz

2.00703018e+08

44482073ea59c80a79722e399cf6df7752c1801f76c4711c673abb240c3bbb9a

Commit history 2

Date Commit Credits Log message

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.

2026-09-26

8cd5ea075a

Jason W. Bacon

biology/py-macs3: Update to 3.0.5

A few fixes and enhancements Changes: https://github.com/macs3-project/MACS/releases Reported by: portscout