biology/atac-seq 0.3.1 FreeBSD

Metaport for ATAC-Seq analysis

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-08
Commit: 2414383046
License: BSD2CLAUSE
Categories: biology, python

Description

Metaport to install tools for typical ATAC-Seq analysis, including QC, adapter trimming, alignment, and differential analysis.

In the other systems

System

Port

Version

FreeBSD

biology/atac-seq

0.3.1

NetBSD

biology/atac-seq

1.5.0

HardenedBSD

biology/atac-seq

0.3.1

Install

Binary package:

pkg install atac-seq

From the ports tree:

cd /usr/ports/biology/atac-seq/ && make install clean

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

RUN_DEPENDS=	atac-seq>0:biology/atac-seq

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	-	-	-	-	-
FreeBSD:14:quarterly	-	-	n/a	-	-
FreeBSD:15:latest	-	0.3.1	n/a	-	-
FreeBSD:15:quarterly	-	0.3.1	n/a	n/a	n/a
FreeBSD:16:latest	-	0.3.1	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

As this port's Makefile names them.

Runtime 14

sra-tools>0 : biology/sra-tools
fastq-trim>0 : biology/fastq-trim
fastqc>0 : biology/fastqc
${PYTHON_PKGNAMEPREFIX}multiqc>0 : biology/py-multiqc
biolibc-tools>0 : biology/biolibc-tools
bwa>0 : biology/bwa
bowtie2>0 : biology/bowtie2
samtools>0 : biology/samtools
${PYTHON_PKGNAMEPREFIX}MACS3>0 : biology/py-macs3
fasda>0 : biology/fasda
fasda-utils>0 : biology/fasda-utils
peak-classifier>0 : biology/peak-classifier
webbrowser>0 : www/webbrowser
curl>0 : ftp/curl

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

Build dependencies 7

Run dependencies 409

The first 100 are listed.

No port depends on this one.

Configuration

No options to configure.

USES: metaport python
Service scripts: none

Files

No file lists for this port.

Commit history 3

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.

2026-07-03

117cd80d6d

Jason W. Bacon

biology/atac-seq: Update to 0.3.1

Drop py-macs2: Incompatible with python 3.12 and unmaintained Install py-macs2 unconditionally

2026-07-01

0d4ebdd15c

Rene Ladan

Mk/bsd.port.mk: mark 14.3 unsupported

all: drop supoprt for FreeBSD 14.3 While here clean up some leftovers from FreeBSD 13 Reviewed by: adamw, jbeich, kirill_varnakov.com, saheed, sunpoet Approved by: portmgr (implicit) Differential Revision: https://reviews.freebsd.org/D57282