| Port details |
- phred Base calling and quality value assignment on DNA sequencing
- 0.020425.c biology
 =2      0.020425.cVersion of this port present on the latest quarterly branch. - Maintainer: mzaki@m.u-tokyo.ac.jp
- Port Added: 2008-05-24 07:05:09
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: PHRED
- WWW:
- http://www.phrap.org/phredphrapconsed.html
- Description:
- Phred reads DNA sequencer trace data, calls bases, assigns quality values
to the bases, and writes the base calls and quality values to output files.
Trace data is read from chromatogram files in the SCF, ABI, and EST formats,
even if they were compressed using gzip, bzip2, or UNIX compress.
Quality values are written to FASTA format files or PHD files, which can be
used by the Phrap sequence assembly program in order to increase the accuracy
of the assembled sequence.
Base calling and quality value accuracies tested for:
ABI models 373, 377, and 3700
Molecular Dynamics MegaBACE
LI-COR 4000
Base calling accuracies tested for:
ABI model 3100
Beckman CEQ
It contains also a data evaluation program called 'daev'.
See DAEV.DOC for more information.
You must obtain the tarball via e-mail to build. See the web site below.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/phred/ && make install clean
- We doubt a package is available for this port because we see it marked as as:
-
Packages are normally not provided for ports that are marked as above.
- To add the package, run one of these commands:
- pkg install biology/phred
- pkg install phred
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (phred-dist-020425.c-acd.tar.Z) = c7a7773447376c024212b680e1ce1e52c30ad8e18dee317ba863bc10db94f6c9
SIZE (phred-dist-020425.c-acd.tar.Z) = 547645
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- This port has no dependencies.
- This port is required by:
- for Run
-
Deleted ports which required this port:
- * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options:- ===> The following configuration options are available for phred-0.020425.c:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
- Options name:
- biology_phred
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
- There is no master site for this port.
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
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) |
0.020425.c
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  ) |
0.020425.c
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
0.020425.c
06 May 2021 11:47:48
|
Mathieu Arnold (mat) |
Deorbit RESTRICTED && NO_CDROM, part two.
Move ports to the licenses framework.
RESTRICTED → auto-accept (unless expressly stated otherwise)
NO_CDROM → dist-mirror pkg-mirror auto-accept
Differential Revision: https://reviews.freebsd.org/D30010 |
0.020425.c
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.020425.c
13 Aug 2019 16:00:39
 |
mat |
Convert to UCL & cleanup pkg-message (categories a-c) |
0.020425.c
10 Sep 2018 13:14:52
|
mat |
Add DOCS options to ports that should have one.
Also various fixes related to said option.
PR: 230864
Submitted by: mat
exp-runs by: antoine |
0.020425.c
23 Aug 2014 18:04:58
|
pi |
update ports:
biology/phrab
biology/phred
biology/consed
Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.
PR: 191336
Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) |
0.020425.c
10 May 2014 18:07:52
|
antoine |
Replace maintainer's email address with one that seems to work
With hat: portmgr |
0.020425.c
03 Jan 2014 15:46:52
|
adamw |
Convert biology to MDOCS and MEXAMPLES |
0.020425.c
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
0.020425.c
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
0.020425.c
25 May 2008 23:05:10
|
edwin |
Teach the building cluster that these ports are not to be build |
0.020425.c
24 May 2008 07:04:45
|
edwin |
New port: biology/consed viewing and editing workbench for sequence
assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> |
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