FreshPorts -- biology/atac-seq: Metaport for ATAC-Seq analysis

atac-seq Metaport for ATAC-Seq analysis

0.3.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.3.0Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer

Port Added: 2023年01月11日 23:48:07

Last Update: 2026年07月04日 00:39:42

Commit Hash: 117cd80

Also Listed In: python

License: NA

WWW:

https://github.com/auerlab/

Description:

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

Homepage cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:

FreshPorts has no man page information for this port.

pkg-plist: as obtained via: make generate-plist

Expand this list (3 items)

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1. /usr/local/share/licenses/atac-seq-0.3.1/catalog.mk
2. /usr/local/share/licenses/atac-seq-0.3.1/LICENSE
3. /usr/local/share/licenses/atac-seq-0.3.1/NA

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USE_RC_SUBR (Service Scripts)

• no SUBR information found for this port

Dependency lines:

• atac-seq>0:biology/atac-seq

To install the port:

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

To add the package, run one of these commands:

• pkg install biology/atac-seq
• pkg install atac-seq

NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.

PKGNAME: atac-seq

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1673549889

---

Packages (timestamps in pop-ups are UTC):

atac-seq

ABI	aarch64	amd64	armv6	armv7	i386	powerpc	powerpc64	powerpc64le
FreeBSD:13:latest	0.3.0	0.3.0	-	-	-	n/a	n/a	n/a
FreeBSD:13:quarterly	0.3.0	0.3.0	-	-	-	n/a	n/a	n/a
FreeBSD:14:latest	-	0.3.1	-	-	-	-	-	-
FreeBSD:14:quarterly	-	0.3.1	-	-	-	-	-	-
FreeBSD:15:latest	-	0.3.1	n/a	-	n/a	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	-	-

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. python3.12 : lang/python312

Test dependencies:

1. python3.12 : lang/python312

Runtime dependencies:

1. sra-tools>0 : biology/sra-tools
2. fastq-trim>0 : biology/fastq-trim
3. fastqc>0 : biology/fastqc
4. py312-multiqc>0 : biology/py-multiqc@py312
5. biolibc-tools>0 : biology/biolibc-tools
6. bwa>0 : biology/bwa
7. bowtie2>0 : biology/bowtie2
8. samtools>0 : biology/samtools
9. py312-MACS3>0 : biology/py-macs3@py312
10. fasda>0 : biology/fasda
11. fasda-utils>0 : biology/fasda-utils
12. peak-classifier>0 : biology/peak-classifier
13. webbrowser>0 : www/webbrowser
14. curl>0 : ftp/curl
15. python3.12 : lang/python312

There are no ports dependent upon this port

---

Configuration Options:

No options to configure

Options name:

biology_atac-seq

USES:

metaport python

FreshPorts was unable to extract/find any pkg message

Master Sites:

1. There is no master site for this port.

biology/atac-seq: Update to 0.3.1
Drop py-macs2: Incompatible with python 3.12 and unmaintained
Install py-macs2 unconditionally

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 

biology/atac-seq: Update to 0.3.0
Add biology/fasda-utils to metaport depends

all: bump PORTREVISION after updating graphics/libyuv
Using the Tools/scripts/bump_revision.pl script

all: remove support for expired FreeBSD 13.3
Reviewed by:	bofh, brnrd, jbeich, nobutaka
Approved by:	portmgr (implicit)
Differential Revision: https://reviews.freebsd.org/D48247 

biology/atac-seq: Update to 0.2.0
Add biology/py-macs3 dep to metaport

biology/atac-seq: Add curl to metaport deps
Standardizing on a download tool simplifies pipelines

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/atac-seq: Drop biology/igv dep
Non-essential and currently broken

biology/atac-seq: Update to 0.1.1
Fix dependency: bowtie -> bowtie2
Add www/webbrowser for portable FastQC report viewing

biology/atac-seq: Metaport for ATAC-Seq analysis
Metaport to install tools for typical ATAC-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.

30 vulnerabilities affecting 415 ports have been reported in the past 14 days

^* - modified, not new

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Last processed:
2026年09月03日 17:10:13 UTC