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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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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
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.
This port has no dependencies.
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:
===> 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:
  1. There is no master site for this port.

Number of commits found: 15

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
1.090518
06 May 2021 11:47:48
commit hash: 3505159e72da2d8313ce2a8ddc527de700b5bc37commit hash: 3505159e72da2d8313ce2a8ddc527de700b5bc37commit hash: 3505159e72da2d8313ce2a8ddc527de700b5bc37commit hash: 3505159e72da2d8313ce2a8ddc527de700b5bc37 files touched by this commit
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
1.090518
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.090518
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.090518
27 May 2020 11:59:13
Revision:536688Original commit files touched by this commit
danfe search for other commits by this committer
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
1.090518
10 Sep 2018 13:14:52
Revision:479406Original commit files touched by this commit
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
1.090518
16 Oct 2014 08:55:30
Revision:370983Original commit files touched by this commit
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
1.090518
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)
0.990329
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
0.990329
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
0.990329
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)
0.990329
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
0.990329
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
0.990329
24 May 2008 07:03:23
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: 15