| Port details |
- py-macs3 Peak caller aimed at transcription factor binding sites
- 3.0.3 biology
 =2      3.0.3Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2024-01-10 15:21:08
- Last Update: 2025-04-09 14:55:11
- Commit Hash: 150c001
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
- Also Listed In: python
- License: BSD3CLAUSE
- WWW:
- https://github.com/taoliu/MACS
- 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.
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- 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:
-
- ${PYTHON_PKGNAMEPREFIX}MACS3>0:biology/py-macs3@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-macs3/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-macs3
- pkg install py311-MACS3
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 py311-MACS3 listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-MACS3
- Package flavors (<flavor>: <package>)
- NOT_FOR_ARCHS: i386
- distinfo:
- TIMESTAMP = 1740145847
SHA256 (macs3-project-MACS-v3.0.3_GH0.tar.gz) = fb5cfe3d8189662b79df7c96f7782bc8327f1aafa61815a2ac86a8337917a558
SIZE (macs3-project-MACS-v3.0.3_GH0.tar.gz) = 198064648
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py311-wheel>0 : devel/py-wheel@py311
- simde>0 : devel/simde
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-scipy>1.11.1 : science/py-scipy@py311
- py311-cykhash>=2.0,<3.0 : devel/py-cykhash@py311
- py311-scikit-learn>=1.3 : science/py-scikit-learn@py311
- py311-hmmlearn>=0.3.2 : math/py-hmmlearn@py311
- py311-cython3>=3.0.12<3.1 : lang/cython3@py311
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Test dependencies:
-
- py311-pytest>0 : devel/py-pytest@py311
- bash : shells/bash
- python3.11 : lang/python311
- perl5>=5.36<5.37 : lang/perl5.36
- Runtime dependencies:
-
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-scipy>1.11.1 : science/py-scipy@py311
- py311-cykhash>=2.0,<3.0 : devel/py-cykhash@py311
- py311-scikit-learn>=1.3 : science/py-scikit-learn@py311
- py311-hmmlearn>=0.3.2 : math/py-hmmlearn@py311
- python3.11 : lang/python311
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-macs3
- USES:
- localbase perl5 python shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 9
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
3.0.3
09 Apr 2025 14:55:11
 |
Po-Chuan Hsieh (sunpoet) |
Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
- Update USE_PYTHON=cython{,_run,_test}
- Convert all cython3 occurrence to USE_PYTHON=cython3*
- While I'm here, fix incorrect usage of combining cython3 in BUILD_DEPENDS and
USE_PYTHON=cython
It is added to simplify the future transition from Cython 0.29 to 3.
The minimal version is set to 3.0.12 because it is required by
devel/py-propcache.
The upper bound of version is set to 3.1 because it is limited by multiple
ports. |
3.0.3
19 Mar 2025 13:45:50
|
Jason W. Bacon (jwb) |
biology/py-macs3: Unbreak package build
pep57 -> distutils
Port passed poudriere before, but spontaneously broke due to
other changes
Reported by: pkg-fallout |
3.0.3
07 Mar 2025 14:28:52
|
Jason W. Bacon (jwb) |
biology/py-macs3: Update to 3.0.3
A few new features and bug fixes
Changes: https://github.com/macs3-project/MACS/releases
Reported by: portscout |
3.0.2
14 Sep 2024 13:23:32
|
Jason W. Bacon (jwb) |
biology/py-macs3: Update to 3.0.2
Some minor enhancements and improved docs
Changes: https://github.com/macs3-project/MACS/releases
Reported by: portscout |
3.0.1
01 Jul 2024 20:27:23
|
Rene Ladan (rene) |
all: drop support for FreeBSD 13.2 which reached EOL today
Thanks again to jbeich for noticing various things I overlooked.
Reviewed by: acm, ashish, eduardo, ehaupt, eugen, jbeich, martymac, mat,
nobukata, sunpoet, tagattie, yuri, arrowd, kde
Differential Revision: https://reviews.freebsd.org/D45141 |
3.0.1
29 Jun 2024 05:02:34
|
Jason E. Hale (jhale) |
*/*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDS
Fix build when setuptools is removed from RUN_DEPENDS in
Mk/Uses/python.mk.
PR: 270510
Approved by: portmgr (blanket) |
3.0.1
18 Apr 2024 23:02:57
|
Jason W. Bacon (jwb) |
biology/py-macs3: Mark not for i386
SIMDE does not support _Float16
Nobody does bioinformatics on 32-bit processors anyway, as many
applications have huge memory requirements |
3.0.1
28 Feb 2024 13:29:15
|
Jason W. Bacon (jwb) |
biology/py-macs3: Update to 3.0.1
Minor bug fix release
Changes: https://github.com/macs3-project/MACS/releases |
3.0.0
10 Jan 2024 15:19:56
|
Jason W. Bacon (jwb) |
biology/py-macs3: Peak caller for TF binding sites
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. |
Number of commits found: 9
|
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