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Port details
consed Graphical tool for editing Phrap assemblies
27.0 biology Deleted 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 View this port on Repology. pkg-fallout 27.0Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2020-05-05
Ignore IGNORE: is marked as broken: unfetchable
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: 2008-05-24 07:01:28
Last Update: 2020-05-05 15:38:12
SVN Revision: 534093
License: not specified in port
WWW:
http://www.phrap.org/consed/consed.html
Description:
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
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

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:
  • consed>0:biology/consed
Conflicts:
CONFLICTS_INSTALL:
  • phd2fasta-[0-9]*
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
No installation instructions:
This port has been deleted.
PKGNAME: consed
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: i386 amd64
distinfo:
SHA256 (consed_linux.tar.gz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc SIZE (consed_linux.tar.gz) = 34390726

No package information for this port in our database
Sometimes this happens. Not all ports have packages.
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. perl5>=5.30.r1<5.31 : lang/perl5.30
Runtime dependencies:
  1. phred : biology/phred
  2. phrap : biology/phrap
  3. linux-c7-xorg-libs>=7.7_7 : x11/linux-c7-xorg-libs
  4. perl5>=5.30.r1<5.31 : lang/perl5.30
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
N/A
USES:
linux perl5 shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
  1. There is no master site for this port.

Number of commits found: 23

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
27.0
05 May 2020 15:38:12
Revision:534093Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
27.0
04 Apr 2020 20:51:41
Revision:530719Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
27.0
06 Nov 2019 12:48:32
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
27.0
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
27.0
05 Sep 2016 19:23:42
Revision:421387Original commit files touched by this commit
tijl search for other commits by this committer
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
  Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
  USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
  ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
  are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling.  In the very rare cases
  that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling.  Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
  default versions framework.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
27.0
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
27.0
26 Dec 2015 13:26:27
Revision:404510Original commit files touched by this commit
rene search for other commits by this committer
biology/consed: undeprecate, it presumably builds fine but it is restricted.

Add a note to ports/LEGAL
27.0
25 Oct 2015 19:35:28
Revision:400160Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
27.0
13 Apr 2015 14:49:38
Revision:383926Original commit files touched by this commit
mat search for other commits by this committer
${ENV} does not exist, it is called ${SETENV}.
27.0
05 Apr 2015 17:55:36
Revision:383309Original commit files touched by this commit
bapt search for other commits by this committer
Mark as broken unfetchable ports
27.0
23 Aug 2014 18:04:58
Revision:365765Original commit files touched by this commit
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)
16.0
29 Jul 2014 19:11:53
Revision:363374Original commit files touched by this commit
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)
16.0
09 Jun 2014 11:21:53
Revision:357139Original commit files touched by this commit
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)
16.0
10 May 2014 18:07:52
Revision:353593Original commit files touched by this commit
antoine search for other commits by this committer
Replace maintainer's email address with one that seems to work

With hat:	portmgr
16.0
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
16.0
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
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)
16.0
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
16.0
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
16.0
07 Sep 2013 07:44:27
Revision:326575Original commit files touched by this commit
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
16.0
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
16.0
19 Mar 2009 17:28:51
Original commit files touched by this commit
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)
16.0
25 May 2008 23:05:10
Original commit files touched by this commit
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
16.0
24 May 2008 07:00:37
Original commit files touched by this commit
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: 23