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Port details
phred Base calling and quality value assignment on DNA sequencing
0.020425.c biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.020425.cVersion of this port present on the latest quarterly branch.
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 2008-05-24 07:05:09
Last Update: 2019-08-13 17:00:39
SVN Revision: 508834
License: not specified in port
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • phred>0:biology/phred
To install the port: cd /usr/ports/biology/phred/ && make install clean
A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted
PKGNAME: phred
Flavors: there is no flavor information for this port.
distinfo:

This port is required by:
for Run
  1. biology/consed

Configuration Options
Master Sites:
  1. There is no master site for this port.

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
13 Aug 2019 16:00:39
Original commit files touched by this commit  0.020425.c
Revision:508834
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
10 Sep 2018 13:14:52
Original commit files touched by this commit  0.020425.c
Revision:479406
mat search for other commits by this committer
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
23 Aug 2014 18:04:58
Original commit files touched by this commit  0.020425.c
Revision:365765
pi search for other commits by this committer
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)
10 May 2014 18:07:52
Original commit files touched by this commit  0.020425.c
Revision:353593
antoine search for other commits by this committer
Replace maintainer's email address with one that seems to work

With hat:	portmgr
03 Jan 2014 15:46:52
Original commit files touched by this commit  0.020425.c
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  0.020425.c
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
19 Mar 2011 12:38:54
Original commit files touched by this commit  0.020425.c

miwi search for other commits by this committer
- Get Rid MD5 support
25 May 2008 23:05:10
Original commit files touched by this commit  0.020425.c

edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:04:45
Original commit files touched by this commit  0.020425.c

edwin search for other commits by this committer
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>

Number of commits found: 9

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