| Port details |
- rainbow Efficient clustering and assembling of short reads, especially for RAD
- 2.0.4 biology
 =2      2.0.4Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-02 16:50:56
- 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: GPLv3+
- WWW:
- https://sourceforge.net/projects/bio-rainbow/
- Description:
- Rainbow provides an ultra-fast and memory-efficient solution to clustering and
assembling short genetic sequence reads produced by Restriction site Associated
DNA Sequencing (RAD-seq). It does this by, first, clustering reads using a
spaced seed method, then it divides potential groups into haplotypes in a
top-down manner. Next, along a guide tree, it iteratively merges sibling
leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses
a greedy algorithm to locally assemble merged reads into contigs. Both optimal
and suboptimal assembly results are output.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- rainbow>0:biology/rainbow
- To install the port:
- cd /usr/ports/biology/rainbow/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/rainbow
- pkg install rainbow
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: rainbow
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1520455667
SHA256 (rainbow_2.0.4.tar.gz) = 79281aae3bccd1ad467afef6fc7c8327aaa8d56f538821e2833d2b8f26b5bafc
SIZE (rainbow_2.0.4.tar.gz) = 77111
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- This port is required by:
- for Run
-
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_rainbow
- USES:
- gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| 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) |
2.0.4
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  ) |
2.0.4
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.0.4
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.0.4
31 Mar 2020 23:18:10
 |
sunpoet |
Update WWW |
2.0.4
02 Apr 2018 16:50:46
|
jwb |
biology/rainbow: Efficient clustering and assembling of short reads
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14924 |
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