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.2414383046
Port details
biology/atac-seq 0.3.1
Metaport for ATAC-Seq analysis
Port info
- Maintainer
- ports@FreeBSD.org
- Packages
- latest: 0.3.1
- Upstream
- Higher version available: 1.5.0
- Last update
- to 0.3.1 · 2414383046
- Quarterly
- not in the 2026Q4 packages
- WWW
- https://github.com/auerlab/
- Links
- cgit · VuXML · Report wrong data
Install
- Package
# pkg install atac-seqinstalls 0.3.1 fromlatest- Port
# cd /usr/ports/biology/atac-seq && make install clean- Size
- 1.6 KiB download · 243 B installed
- License
- NA
- pkg-message
Shown always
===> NOTICE: The atac-seq port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Packages by version and architecture
latest
| FreeBSD version | amd64 | aarch64 | i386 |
|---|---|---|---|
| FreeBSD 16 | 0.3.1 | ✗ | – |
| FreeBSD 15 | ✗ | ✗ | – |
| FreeBSD 14 | ✗ | ✗ | ✗ |
quarterly (2026Q4)
| FreeBSD version | amd64 | aarch64 | i386 |
|---|---|---|---|
| FreeBSD 15 | ✗ | ✗ | – |
| FreeBSD 14 | ✗ | ✗ | ✗ |
version as in the ports tree (latest) or the most common one (quarterly) · different version · ✗ not built · – no packages for this platform. Package sets that have not been rebuilt for 60 days are left out.
Dependencies
Depends on 15
- lang/python312 3.12.15 12 unaddressed
- biology/biolibc-tools 0.1.5
- biology/bowtie2 2.5.5
- biology/bwa 0.7.19
- biology/fasda 0.2.0.1
- biology/fasda-utils 0.1.0.2_1
- biology/fastq-trim 0.1.4
- biology/fastqc 0.12.1_2
- biology/peak-classifier 0.1.4.13_2
- biology/py-macs3 3.0.5
- biology/py-multiqc 1.35
- biology/samtools 1.24
- biology/sra-tools 3.4.1_3
- ftp/curl 8.23.0
- www/webbrowser 0.4.0
Run and library dependencies of the package on latest. Build dependencies are not in the package index.
Required by 0
No package on latest depends on it.
Packages on latest that depend on it directly.
Unaddressed and VuXML only (0)
No unaddressed CVE and nothing reported by
pkg audit for the packaged version 0.3.1.Fixed (0)
No VuXML entries for this package.
Problem reports (0) · open in Bugzilla, most recently changed first
None.
Commits (12)
biology/atac-seq: Update to 0.3.1 Drop py-macs2: Incompatible with python 3.12 and unmaintained Install py-macs2 unconditionally117cd80d6d
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/D572820d4ebdd15c
biology/atac-seq: Update to 0.3.0 Add biology/fasda-utils to metaport depends746a50b935
all: bump PORTREVISION after updating graphics/libyuv Using the Tools/scripts/bump_revision.pl scriptb304d8ab18
all: remove support for expired FreeBSD 13.3 Reviewed by: bofh, brnrd, jbeich, nobutaka Approved by: portmgr (implicit) Differential Revision: https://reviews.freebsd.org/D482478777dde246
biology/atac-seq: Update to 0.2.0 Add biology/py-macs3 dep to metaport999c86b251
biology/atac-seq: Add curl to metaport deps Standardizing on a download tool simplifies pipelines3ef8325ef6
*: Bump PORTREVISIONs for math/mpc update to 1.3.18d3e020ed0
biology/atac-seq: Drop biology/igv dep Non-essential and currently brokenada9b15851
biology/atac-seq: Update to 0.1.1 Fix dependency: bowtie -> bowtie2 Add www/webbrowser for portable FastQC report viewingff57c60617
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.d2c13cc6fd