| Port details |
- phd2fasta Converter from output files of Phred/Consed to FASTA files
- 0.990622.f biology
 =0      0.990622.fVersion of this port present on the latest quarterly branch.  DEPRECATED: Not staged. See http://lists.freebsd.org/pipermail/freebsd-ports-announce/2014-May/000080.html
 This port expired on: 2014-08-31
 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: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
- 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
- Port Added: 2008-05-24 07:02:33
- Last Update: 2014-09-02 12:45:02
- SVN Revision: 366995
- License: not specified in port
- WWW:
- http://www.phrap.org/phredphrapconsed.html
- Description:
- 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
 cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- phd2fasta>0:biology/phd2fasta
- No installation instructions:
- This port has been deleted.
- PKGNAME: phd2fasta
- Flavors: there is no flavor information for this port.
- distinfo:
- There is no distinfo for this port.
No package information for this port in our database- Sometimes this happens. Not all ports have packages.
- This port has no dependencies.
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- N/A
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 10
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.990622.f
02 Sep 2014 12:45:02
  |
bapt |
Second run at cleaning out non staged ports without pending PR |
0.990622.f
23 Jul 2014 16:44:28
|
bapt |
Reset maintainership for ports not staged with no pending PR
With hat: portmgr |
0.990622.f
09 Jun 2014 11:21:53
|
olgeni |
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) |
0.990622.f
10 May 2014 18:07:52
|
antoine |
Replace maintainer's email address with one that seems to work
With hat: portmgr |
0.990622.f
03 Jan 2014 15:46:52
|
adamw |
Convert biology to MDOCS and MEXAMPLES |
0.990622.f
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
0.990622.f
26 Apr 2013 16:23:14
|
bdrewery |
Remove unneeded escaping |
0.990622.f
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
0.990622.f
25 May 2008 23:05:10
|
edwin |
Teach the building cluster that these ports are not to be build |
0.990622.f
24 May 2008 07:01:56
|
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> |
Number of commits found: 10
|
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