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Port details
phrap Phrap is a 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
Ignore IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/local/PORTS-head/distfiles/phrap, and then try it again
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 24 May 2008 07:03:43
License: not specified in port
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.

WWW: http://www.phrap.org/phredphrapconsed.html
SVNWeb : Homepage : PortsMon

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: phrap

distinfo:

SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665
SIZE (phrap/distrib.tar.gz) = 333159

This port is required by:

for Run * - 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
     No options to configure

Master Sites:
    There is no master site for this port.

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Oct 2014 08:55:30
Original commit files touched by this commit  1.090518
Revision:370983
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  1.090518
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)
10 May 2014 18:07:52
Original commit files touched by this commit  0.990329
Revision:353593
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  0.990329
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  0.990329
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)
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: 8

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