| Port details |
- lagan Efficient tools for large-scale multiple alignments of genomic DNA
- 2.0_2 biology
 =0      2.0_2Version of this port present on the latest quarterly branch.  DEPRECATED: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
 This port expired on: 2021-04-01
- There is no maintainer for this port.
- Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
- Port Added: 2006-03-16 22:31:50
- Last Update: 2021-04-07 17:54:26
- Commit Hash: 5980fd4
- License: GPLv2
- WWW:
- http://lagan.stanford.edu/
- Description:
- The Lagan Tookit is a set of alignment programs for comparative
genomics. The three main components are a pairwise aligner (LAGAN), a
multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All
three are based on the CHAOS local alignment tool and combine speed
(regions up to several megabases can be aligned in minutes) with high
accuracy. The results of the alignment can be visualized using the VISTA
visualization tool.
WWW: http://lagan.stanford.edu/
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: lagan
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (lagan20.tar.gz) = a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
SIZE (lagan20.tar.gz) = 589115
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Runtime dependencies:
-
- perl5>=5.32.r0<5.33 : lang/perl5.32
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_lagan
- USES:
- perl5 shebangfix
- 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 |
|---|
2.0_2
07 Apr 2021 17:54:26
 |
Rene Ladan (rene) |
Remove expired ports:
2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11) (Only the first 15 lines of the commit message are shown above  ) |
2.0_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.0_2
30 Aug 2020 09:47:50
  |
zeising |
Extend expiration of ports broken with -fno-common
Extend the expiration of unmaintained leaf ports that are broken with
-fno-common and previously had a short expiration date. The new date is set
to 2021-04-01, meaning the ports will be in the 2021Q2 branch, giving people
until 2021-06-30 (10 months from now) to fix issues.
Improve the wording of the deprecation message, mentioning both llvm 11 and
-fno-common.
Bump portrevision to force reinstall. This way the warning message about
deprecation will be displayed to users installing or reinstalling the
software.
MFH: 2020Q3 (maybe) |
2.0_1
29 Aug 2020 08:34:52
|
tcberner |
biology/: Fix build with clang11 and deprecate ports@ ports |
2.0_1
13 Aug 2019 16:00:39
|
mat |
Convert to UCL & cleanup pkg-message (categories a-c) |
2.0_1
19 May 2016 11:09:14
|
amdmi3 |
- Fix trailing whitespace in pkg-messages
Approved by: portmgr blanket |
2.0_1
11 May 2016 21:48:50
|
bapt |
Prevent collision with getline(3)
While here regen patches |
2.0_1
09 Jan 2016 18:26:40
|
pawel |
Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRS |
2.0_1
11 Jun 2015 10:17:25
|
amdmi3 |
- Fix shebangs
MFH: 2015Q2 |
2.0
27 Nov 2013 13:16:48
|
jadawin |
- Fix build
- Support STAGEDIR
PR: ports/184238
Submitted by: KATO Tsuguru <tkato432@yahoo.com> |
2.0
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
2.0
03 Aug 2013 13:44:01
 |
mat |
- Convert to new perl framework
- Remove MAKE_JOBS_SAFE=yes, it's the default. |
2.0
15 Nov 2012 07:04:29
|
wen |
- Update to version 2.0
- Update pkg-descr
PR: 172497
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Feature safe: yes |
1.2
01 Oct 2012 14:45:17
|
tabthorpe |
- Reassign to the heap at maintainer's request |
1.2
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
1.2
08 Nov 2010 15:05:11
|
pav |
- Unbreak build: CPP is now part of MAKE_ENV
Reported by: pointyhat |
1.2
25 Jul 2008 09:08:42
|
pav |
- Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default
MAKE_ENV |
1.2
16 Mar 2006 22:31:26
|
garga |
Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.
PR: ports/93058
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> |
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