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Port details
consed Graphical tool for editing Phrap assemblies
27.0 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
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 24 May 2008 07:01:28
License: not specified in port
Consed is a tool for viewing and editing sequence assemblies made by phrap,
and includes Autofinish which will automatically choose finishing reads.

WWW: http://www.phrap.org/consed/consed.html
SVNWeb : Homepage : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. /usr/local/bin/perl5.16.3 : lang/perl5.16
Runtime dependencies:
  1. phred : biology/phred
  2. phrap : biology/phrap
  3. /compat/linux/etc/fedora-release : emulators/linux_base-f10
  4. /compat/linux/lib/libexpat.so.1 : textproc/linux-f10-expat
  5. /compat/linux/usr/lib/libfontconfig.so.1.3.0 : x11-fonts/linux-f10-fontconfig
  6. /compat/linux/usr/lib/libXrandr.so.2.1.0 : x11/linux-f10-xorg-libs
  7. /usr/local/bin/perl5.16.3 : lang/perl5.16
There are no ports dependent upon this port

To install the port: cd /usr/ports/biology/consed/ && 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://bozeman.mbt.washington.edu/consed/distributions/27.0/
  2. http://distcache.FreeBSD.org/ports-distfiles/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Aug 2014 18:04:58
Original commit files touched by this commit  27.0
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)
29 Jul 2014 19:11:53
Original commit files touched by this commit  16.0
Revision:363374
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
09 Jun 2014 11:21:53
Original commit files touched by this commit  16.0
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  16.0
Revision:353593
antoine search for other commits by this committer
Replace maintainer's email address with one that seems to work

With hat:	portmgr
21 Feb 2014 13:35:26
Original commit files touched by this commit  16.0
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  16.0
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  16.0
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  16.0
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)
07 Sep 2013 07:44:27
Original commit files touched by this commit  16.0
Revision:326575
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
19 Mar 2011 12:38:54
Original commit files touched by this commit  16.0
miwi search for other commits by this committer
- Get Rid MD5 support
19 Mar 2009 17:28:51
Original commit files touched by this commit  16.0
bsam search for other commits by this committer
Welcome to the new linux ports infrastructure which allows using
both current (fc4) and future linux (f8) distributions at one
ports tree.

The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.

The idea was taken from bsd.gnome.mk and others.

More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.

Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.

Other changes are coming. Stay tuned!

PR:             ports/132510
Submitted by:   bsam (me)
Exp-run by:     portmgr (pav)
25 May 2008 23:05:10
Original commit files touched by this commit  16.0
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:00:37
Original commit files touched by this commit  16.0
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: 13

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