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Port details
phd2fasta 0.990622.f biology on this many watch lists=0 search for ports that depend on this port
Deprecated DEPRECATED: Not staged. See http://lists.freebsd.org/pipermail/freebsd-ports-announce/2014-May/000080.html
Expiration Date EXPIRATION DATE: 2014-08-31
Ignore IGNORE: you must request the source code (phd2fasta-acd-dist.tar.Z) via e-mail, place it manually in /usr/local/PORTS-head/distfiles, and then try it again
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Converter from output files of Phred/Consed to FASTA files

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 24 May 2008 07:02:33
License: not specified in port


Phred and consed write sequence and quality value information in
'phd' output files. A phd file contains information in a header,
the called bases, the base quality values, and the base call trace
locations.  Phd2fasta reads phd files and writes sequence and quality
value FASTA files, which phrap and cross_match need as input.
(Consed needs phd files in order to obtain the base call locations.)

WWW: http://www.phrap.org/phredphrapconsed.html
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

To install the port: cd /usr/ports/biology/phd2fasta/ && make install clean

A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted


Configuration Options
     No options to configure

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Jul 2014 16:44:28
Original commit files touched by this commit  0.990622.f
Revision:362705
bapt search for other commits by this committer
Reset maintainership for ports not staged with no pending PR

With hat:	portmgr
09 Jun 2014 11:21:53
Original commit files touched by this commit  0.990622.f
Revision:357139
olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
10 May 2014 18:07:52
Original commit files touched by this commit  0.990622.f
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  0.990622.f
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  0.990622.f
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)
26 Apr 2013 16:23:14
Original commit files touched by this commit  0.990622.f
Revision:316622
bdrewery search for other commits by this committer
Remove unneeded escaping
19 Mar 2011 12:38:54
Original commit files touched by this commit  0.990622.f
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  0.990622.f
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:01:56
Original commit files touched by this commit  0.990622.f
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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