BSD Portsbiology/ddocent 2.7.8_5 GhostBSD
Bash pipeline for RAD sequencing
- System
- GhostBSD
- Repository
- GhostBSD
- Maintainer
- [email protected] (as in FreeBSD)
- License
- MIT
- Categories
- biology, java, perl5, python
- Package size
- 26.8 KiB, 176.6 KiB installed
Description
dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set. It is designed to run on Linux based machines with large memory capacity and multiple processing cores, and it can be modified for use on HPC.
In the other systems
The newest version among them is 2.7.8, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| GhostBSD | biology/ddocent | 2.7.8_5 newest | none known | - | [email protected] | - |
| NetBSD | wip/ddocent by name | 2.5.2 | none known | - | [email protected] | - |
Install
Binary package:
pkg install dDocentDependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
Run dependencies 24
- biology/bamtools
- biology/bedtools
- biology/bwa
- biology/cd-hit
- biology/fastp
- biology/freebayes
- biology/pear-merger
- biology/rainbow
- biology/samtools
- biology/seqtk
- biology/stacks
- biology/trimadap
- biology/trimmomatic
- biology/vcflib
- biology/vcftools
- java/openjdk25
- lang/gawk
- lang/mawk
- lang/perl5.42
- lang/python312
- math/gnuplot
- shells/bash
- sysutils/coreutils
- sysutils/parallel
No port depends on this one.
Configuration
No options to configure.
- Service scripts
- none
Message after installing
===> NOTICE: The dDocent 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 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: No apparent interest, unable to maintain. It is scheduled to be removed on or after 2026-09-30.