| Port details |
- chip-seq Metaport for ChIP-Seq analysis
- 0.3.1 biology
 =0      0.1.2_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2023-06-14 21:24:35
- Last Update: 2026-07-04 00:42:57
- Commit Hash: 4503d4f
- Also Listed In: python
- License: NA
- WWW:
- https://github.com/auerlab/
- Description:
- Metaport to install tools for typical ChIP-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- Dependency lines:
-
- chip-seq>0:biology/chip-seq
- To install the port:
- cd /usr/ports/biology/chip-seq/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/chip-seq
- pkg install chip-seq
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: chip-seq
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1673549889
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:
-
- python3.12 : lang/python312
- Test dependencies:
-
- python3.12 : lang/python312
- Runtime dependencies:
-
- sra-tools>0 : biology/sra-tools
- fastq-trim>0 : biology/fastq-trim
- fastqc>0 : biology/fastqc
- py312-multiqc>0 : biology/py-multiqc@py312
- biolibc-tools>0 : biology/biolibc-tools
- bwa>0 : biology/bwa
- bowtie2>0 : biology/bowtie2
- samtools>0 : biology/samtools
- py312-MACS3>0 : biology/py-macs3@py312
- fasda>0 : biology/fasda
- fasda-utils>0 : biology/fasda-utils
- peak-classifier>0 : biology/peak-classifier
- webbrowser>0 : www/webbrowser
- curl>0 : ftp/curl
- python3.12 : lang/python312
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_chip-seq
- USES:
- metaport python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
- There is no master site for this port.
|
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 |
|---|
0.3.1
04 Jul 2026 00:42:57
 |
Jason W. Bacon (jwb) |
biology/chip-seq: Update to 0.3.1
Drop py-macs2: Incompatible with python 3.12 and unmaintained
Install py-macs2 unconditionally |
0.1.2_1
31 Aug 2025 10:30:51
|
Rene Ladan (rene) |
all: bump PORTREVISION after updating graphics/libyuv
Using the Tools/scripts/bump_revision.pl script |
0.1.2
14 Jun 2023 21:23:37
|
Jason W. Bacon (jwb) |
biology/chip-seq: Metaport for ChIP-Seq analysis
Metaport to install tools for typical ChIP-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
Presently identical to biology/atac-seq, but may diverge in the future. |
Number of commits found: 3
|
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