| Port details |
- phrap Program for assembling shotgun DNA sequence data
- 1.090518 biology
 =2      1.090518Version of this port present on the latest quarterly branch.  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
- Port Added: 2008-05-24 07:03:43
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: PHRAP
- WWW:
- http://www.phrap.org/phredphrapconsed.html
- Description:
- Phrap is a program for assembling shotgun DNA sequence data.
Among other features, it allows use of the entire read and not just the
trimmed high quality part, it uses a combination of user-supplied and
internally computed data quality information to improve assembly accuracy
in the presence of repeats, it constructs the contig sequence as a mosaic
of the highest quality read segments rather than a consensus, it provides
extensive assembly information to assist in trouble-shooting assembly
problems, and it handles large datasets.
This package also contains Swat and Cross_match.
Swat is a program for searching one or more DNA or protein query sequences
against a sequence database, using (an efficient implementation of) the
Smith-Waterman-Gotoh algorithm.
Cross_Match is a general-purpose utility based on Swat for comparing any
two sets of DNA sequences, and it can be used to:
* produce vector-masked versions of a set of reads
* compare a set of cDNA sequences to a set of cosmids
* compare contigs found by two altanative assembly procedures to each other
* compare phrap contigs to the final edited cosmid sequence.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/phrap/ && make install clean
- We doubt a package is available for this port because we see it marked as as:
- Ignore
- Package not available
Packages are normally not provided for ports that are marked as above.- To add the package, run one of these commands:
- pkg install biology/phrap
- pkg install phrap
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665
SIZE (phrap/distrib.tar.gz) = 333159
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- This port has no dependencies.
- This port is required by:
- for Run
-
Deleted ports which required this port:
- * - 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:- ===> The following configuration options are available for phrap-1.090518:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
- Options name:
- biology_phrap
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
- There is no master site for this port.
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
07 Sep 2022 21:58:51
 |
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
1.090518
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
1.090518
06 May 2021 11:47:48
|
Mathieu Arnold (mat) |
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 |
1.090518
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
1.090518
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.090518
27 May 2020 11:59:13
 |
danfe |
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1). |
1.090518
10 Sep 2018 13:14:52
|
mat |
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 |
1.090518
16 Oct 2014 08:55:30
|
ak |
- 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 |
1.090518
23 Aug 2014 18:04:58
|
pi |
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) |
0.990329
10 May 2014 18:07:52
|
antoine |
Replace maintainer's email address with one that seems to work
With hat: portmgr |
0.990329
03 Jan 2014 15:46:52
|
adamw |
Convert biology to MDOCS and MEXAMPLES |
0.990329
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
0.990329
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
0.990329
25 May 2008 23:05:10
|
edwin |
Teach the building cluster that these ports are not to be build |
0.990329
24 May 2008 07:03:23
|
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> |
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