| Port details |
- ddocent Bash pipeline for RAD sequencing
- 2.7.8_2 biology
 =2      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: 2024-12-31 08:57:55
- Commit Hash: 0835676
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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:
-
- python3.11 : lang/python311
- perl5>=5.36<5.37 : lang/perl5.36
- Test dependencies:
-
- python3.11 : lang/python311
- 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
- python3.11 : lang/python311
- perl5>=5.36<5.37 : lang/perl5.36
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_ddocent
- USES:
- java perl5 python shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 11
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.7.8_2
31 Dec 2024 08:57:55
 |
Muhammad Moinur Rahman (bofh) |
Mk/**java.mk: Convert bsd.java.mk to USES
The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
USES=java:build,run if NO_BUILD is undefined. Else it defaults to
USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>
Approved by: mat (portmgr), glewis
Differential Revision: https://reviews.freebsd.org/D48201 |
2.7.8_2
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.7.8_1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
2.7.8_1
30 Sep 2021 21:23:30
|
Rene Ladan (rene) |
cleanup: drop support for EOL FreeBSD 11.X
Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11
Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*
Reviewed by: doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index |
2.7.8_1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.7.8_1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.7.8_1
26 Jul 2019 20:46:57
 |
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
2.7.8
04 May 2019 15:09:10
|
jwb |
biology/ddocent: Upgrade to 2.7.8
Reported by: portscout |
2.2.25_1
12 Dec 2018 01:35:36
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
2.2.25
20 Apr 2018 01:34:05
|
jwb |
biology/ddocent: Bash pipeline for RAD sequencing
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15139 |
Number of commits found: 11
|
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