| Port details |
- py-macs3 Peak caller aimed at transcription factor binding sites
- 3.0.1 biology
 =0      3.0.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2024-01-10 15:21:08
- Last Update: 2024-04-18 23:02:57
- Commit Hash: 6308879
- 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.
  ¦  ¦  ¦  ¦ 
- 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 py39-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 py39-MACS3 listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-MACS3
- Package flavors (<flavor>: <package>)
- NOT_FOR_ARCHS: i386
- distinfo:
- TIMESTAMP = 1713397031
SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce
SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439
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:
-
- py39-wheel>0 : devel/py-wheel@py39
- py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
- simde>0 : devel/simde
- py39-cykhash>0 : devel/py-cykhash@py39
- py39-hmmlearn>0 : math/py-hmmlearn@py39
- cython-3.9 : lang/cython@py39
- python3.9 : lang/python39
- py39-build>=0 : devel/py-build@py39
- py39-installer>=0 : devel/py-installer@py39
- Test dependencies:
-
- py39-pytest>0 : devel/py-pytest@py39
- bash : shells/bash
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
- py39-cykhash>0 : devel/py-cykhash@py39
- py39-hmmlearn>0 : math/py-hmmlearn@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/atac-seq
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: 3
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
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: 3
|
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