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Port details
phrap Program for assembling shotgun DNA sequence data
1.090518 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 View this port on Repology. pkg-fallout 1.090518Version of this port present on the latest quarterly branch.
Ignore IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/ports/distfiles/phrap, and then try it again
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 2008-05-24 07:03:43
Last Update: 2021-05-06 11:47:48
Commit Hash: 3505159
License: PHRAP
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (15 items)
Collapse this list.
  1. /usr/local/share/licenses/phrap-1.090518/catalog.mk
  2. /usr/local/share/licenses/phrap-1.090518/LICENSE
  3. /usr/local/share/licenses/phrap-1.090518/PHRAP
  4. @mode 111
  5. bin/calf_merge
  6. bin/pcluster
  7. bin/cross_match
  8. bin/loco
  9. bin/phrap
  10. bin/phrapview
  11. bin/swat
  12. @mode
  13. @owner
  14. @group
  15. @mode
Collapse this list.
Dependency lines:
  • phrap>0:biology/phrap
To install the port:
cd /usr/ports/biology/phrap/ && make install clean
A package is not available for ports marked as:
Forbidden / Broken / Ignore / Restricted
PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
Flavors: there is no flavor information for this port.
distinfo:
No package information for this port in our database
Sometimes this happens. Not all ports have packages.

This port is required by:
for Run

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/consed*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
Options name:
FreshPorts was unable to extract/find any pkg message
Master Sites:
  1. There is no master site for this port.

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 May 2021 11:47:48
 files touched by this commit commit hash:3505159e72da2d8313ce2a8ddc527de700b5bc37  1.090518
Mathieu Arnold (mat) search for other commits by this committer
Deorbit RESTRICTED && NO_CDROM, part two.

Move ports to the licenses framework.

RESTRICTED → auto-accept (unless expressly stated otherwise)
NO_CDROM → dist-mirror pkg-mirror auto-accept

Differential Revision:  https://reviews.freebsd.org/D30010
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  1.090518
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.090518
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
27 May 2020 11:59:13
Original commit files touched by this commit Revision:536688  1.090518
danfe search for other commits by this committer
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
10 Sep 2018 13:14:52
Original commit files touched by this commit Revision:479406  1.090518
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
16 Oct 2014 08:55:30
Original commit files touched by this commit Revision:370983  1.090518
ak search for other commits by this committer
- Fix various distinfo errors
- Remove unused USE_* knobs
- Fix typos in USE_* knobs
- Remove empty lines after .include <bsd.port.mk>

Approved by:	portmgr (bapt)
Differential Revision:	https://reviews.freebsd.org/D911
23 Aug 2014 18:04:58
Original commit files touched by this commit Revision:365765  1.090518
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 Revision:353593  0.990329
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 Revision:338550  0.990329
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 Revision:327709  0.990329
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   0.990329
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   0.990329
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:03:23
Original commit files touched by this commit   0.990329
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