| Port details on branch 2022Q3 |
- ddocent Bash pipeline for RAD sequencing
- 2.7.8_2 biology
 =0      2.7.8_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-20 01:34:22
- Last Update: 2023-04-23 09:09:58
- Commit Hash: 8d3e020
- Also Listed In: java perl5 python
- License: MIT
- WWW:
- http://ddocent.com
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- dDocent>0:biology/ddocent
- To install the port:
- cd /usr/ports/biology/ddocent/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/ddocent
- pkg install dDocent
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: dDocent
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1556888100
SHA256 (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 02aa297f602b55587782c959379cada8d8b0570973da75eb9f5786089a3ed485
SIZE (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 345571
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
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- mawk>=0 : lang/mawk
- gawk>=0 : lang/gawk
- coreutils>=0 : sysutils/coreutils
- gnuplot>=0 : math/gnuplot
- parallel>=0 : sysutils/parallel
- bash : shells/bash
- bwa>=0.7.13 : biology/bwa
- cd-hit>=0 : biology/cd-hit
- samtools>=1.3 : biology/samtools
- vcftools>=0.1.15 : biology/vcftools
- trimmomatic>=0 : biology/trimmomatic
- bamtools>=0 : biology/bamtools
- stacks>=0 : biology/stacks
- rainbow>=0 : biology/rainbow
- trimadap>=0 : biology/trimadap
- seqtk>=0 : biology/seqtk
- bedtools>=2.26.0 : biology/bedtools
- pear-merger>=0 : biology/pear-merger
- vcflib>=0 : biology/vcflib
- freebayes : biology/freebayes
- fastp : biology/fastp
- java : java/openjdk8
- python3.9 : lang/python39
- perl5>=5.32.r0<5.33 : lang/perl5.32
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_ddocent
- USES:
- perl5 python shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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