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Port details
lagan Efficient tools for large-scale multiple alignments of genomic DNA
2.0_2 biology Deleted 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 2.0_2Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
Expired 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 search for ports maintained by this maintainer
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/
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (44 items)
Collapse this list.
  1. lagan/anchors
  2. lagan/chaos
  3. lagan/glocal
  4. lagan/mlagan
  5. lagan/order
  6. lagan/anal_gloc.pl
  7. lagan/lagan.pl
  8. lagan/rechaos.pl
  9. lagan/slagan.pl
  10. lagan/utils/Glue
  11. lagan/utils/bin2bl
  12. lagan/utils/bin2mf
  13. lagan/utils/cextract
  14. lagan/utils/contigorder
  15. lagan/utils/cstat
  16. lagan/utils/dotplot
  17. lagan/utils/fa2xfa
  18. lagan/utils/getbounds
  19. lagan/utils/getcontigpos
  20. lagan/utils/getlength
  21. lagan/utils/getoverlap
  22. lagan/utils/rc
  23. lagan/utils/scorealign
  24. lagan/utils/scorecontigs
  25. lagan/utils/seqmerge
  26. lagan/utils/cmerge2.pl
  27. lagan/utils/draft.pl
  28. lagan/utils/mextract.pl
  29. lagan/utils/mf2bin.pl
  30. lagan/utils/mpretty.pl
  31. lagan/utils/mproject.pl
  32. lagan/utils/mrun.pl
  33. lagan/utils/mrunfile.pl
  34. lagan/utils/mrunpairs.pl
  35. lagan/utils/mviz.pl
  36. lagan/Readmes/README.FIRST
  37. lagan/Readmes/README.chaos
  38. lagan/Readmes/README.lagan
  39. lagan/Readmes/README.mlagan
  40. lagan/Readmes/README.tools
  41. lagan/Readmes/README.shuffle
  42. /usr/local/share/licenses/lagan-2.0_2/catalog.mk
  43. /usr/local/share/licenses/lagan-2.0_2/LICENSE
  44. /usr/local/share/licenses/lagan-2.0_2/GPLv2
Collapse this list.
Dependency lines:
  • lagan>0:biology/lagan
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):
lagan
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--2.0_2---2.0_2-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. http://lagan.stanford.edu/lagan_web/
Collapse this list.
Port Moves
  • port deleted on 2021-04-07
    REASON: Has expired: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)

Number of commits found: 18

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.0_2
07 Apr 2021 17:54:26
commit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06e files touched by this commit
Rene Ladan (rene) search for other commits by this committer
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 View all of this commit message)
2.0_2
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.
2.0_2
30 Aug 2020 09:47:50
Revision:547044Original commit files touched by this commit
zeising search for other commits by this committer
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
Revision:546885Original commit files touched by this commit
tcberner search for other commits by this committer
biology/: Fix build with clang11 and deprecate ports@ ports
2.0_1
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
2.0_1
19 May 2016 11:09:14
Revision:415503Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
2.0_1
11 May 2016 21:48:50
Revision:415036Original commit files touched by this commit
bapt search for other commits by this committer
Prevent collision with getline(3)
While here regen patches
2.0_1
09 Jan 2016 18:26:40
Revision:405652Original commit files touched by this commit
pawel search for other commits by this committer
Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRS
2.0_1
11 Jun 2015 10:17:25
Revision:389186Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix shebangs

MFH:		2015Q2
2.0
27 Nov 2013 13:16:48
Revision:335011Original commit files touched by this commit
jadawin search for other commits by this committer
- Fix build
- Support STAGEDIR

PR:		ports/184238
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2.0
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)
2.0
03 Aug 2013 13:44:01
Revision:324191Original commit files touched by this commit Sanity Test Failure
mat search for other commits by this committer
- Convert to new perl framework
- Remove MAKE_JOBS_SAFE=yes, it's the default.
2.0
15 Nov 2012 07:04:29
Revision:307436Original commit files touched by this commit
wen search for other commits by this committer
- 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
Revision:305130Original commit files touched by this commit
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
1.2
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
1.2
08 Nov 2010 15:05:11
Original commit files touched by this commit
pav search for other commits by this committer
- Unbreak build: CPP is now part of MAKE_ENV

Reported by:    pointyhat
1.2
25 Jul 2008 09:08:42
Original commit files touched by this commit
pav search for other commits by this committer
- Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default
MAKE_ENV
1.2
16 Mar 2006 22:31:26
Original commit files touched by this commit
garga search for other commits by this committer
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>

Number of commits found: 18