| Port details |
- atac-seq Metaport for ATAC-Seq analysis
- 0.2.0 biology
 =2      0.2.0Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2023-01-11 23:48:07
- Last Update: 2024-01-10 16:05:41
- Commit Hash: 999c86b
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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 = 1704902712
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:
-
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- sra-tools>0 : biology/sra-tools
- fastq-trim>0 : biology/fastq-trim
- fastqc>0 : biology/fastqc
- py39-multiqc>0 : biology/py-multiqc@py39
- biolibc-tools>0 : biology/biolibc-tools
- bwa>0 : biology/bwa
- bowtie2>0 : biology/bowtie2
- samtools>0 : biology/samtools
- py39-macs2>0 : biology/py-macs2@py39
- fasda>0 : biology/fasda
- peak-classifier>0 : biology/peak-classifier
- webbrowser>0 : www/webbrowser
- curl>0 : ftp/curl
- py39-MACS3>0 : biology/py-macs3@py39
- python3.9 : lang/python39
- 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:
- There is no master site for this port.
|
Number of commits found: 6
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.2.0
10 Jan 2024 16:05:41
 |
Jason W. Bacon (jwb) |
biology/atac-seq: Update to 0.2.0
Add biology/py-macs3 dep to metaport |
0.1.3
28 Jul 2023 14:35:04
|
Jason W. Bacon (jwb) |
biology/atac-seq: Add curl to metaport deps
Standardizing on a download tool simplifies pipelines |
0.1.2_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.1.2
19 Feb 2023 18:11:12
|
Jason W. Bacon (jwb) |
biology/atac-seq: Drop biology/igv dep
Non-essential and currently broken |
0.1.1
12 Jan 2023 19:00:03
|
Jason W. Bacon (jwb) |
biology/atac-seq: Update to 0.1.1
Fix dependency: bowtie -> bowtie2
Add www/webbrowser for portable FastQC report viewing |
0.1.0
11 Jan 2023 23:47:02
|
Jason W. Bacon (jwb) |
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. |
Number of commits found: 6
|
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