| Port details |
- sim4 Algorithm for aligning expressed DNA with genomic sequences
- 2003.09.21_1 biology
 =0      2003.09.21_1Version of this port present on the latest quarterly branch.  DEPRECATED: Upstream last update was in 2005
 This port expired on: 2024-01-17
- 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: 2000-07-27 11:33:01
- Last Update: 2024-01-18 18:29:13
- Commit Hash: b8f4ba2
- License: GPLv2
- WWW:
- http://globin.cse.psu.edu/
- Description:
- This package implements the Sim4 algorithm for aligning expressed DNA
with genomic sequences, described in the paper:
L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
"A computer program for aligning a cDNA sequence with a genomic DNA sequence."
Genome Research 8, 967-974.
Port maintained by the FreeBSD bio-porters mailing list.
  ¦  ¦  ¦  ¦ 
- 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: sim4
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (sim4.2003-09-21.tar.gz) = 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee
SIZE (sim4.2003-09-21.tar.gz) = 60814
Packages (timestamps in pop-ups are UTC):
- This port has no dependencies.
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_sim4
- 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 |
|---|
2003.09.21_1
18 Jan 2024 18:29:13
 |
Muhammad Moinur Rahman (bofh) |
biology/sim4: Remove expired port
2024-01-17 biology/sim4: Upstream last update was in 2005 |
2003.09.21_1
18 Dec 2023 08:29:31
|
Rene Ladan (rene) |
biology/sim4: fix EXPIRATION_DATE |
2003.09.21_1
17 Dec 2023 13:11:36
|
Muhammad Moinur Rahman (bofh) |
biology/sim4: Mark DEPRECATED
- Upstream last update was in 2005
- Set EXPIRATION_DATE 2024-01-17 |
2003.09.21_1
08 Sep 2022 15:46:38
|
Stefan Eßer (se) |
Remove WWW lines that have been moved into Makefiles
Approved by: portmgr (implicit) |
2003.09.21_1
08 Sep 2022 15:43:21
|
Stefan Eßer (se) |
Move more WWW entries from pkg-descr files into Makefiles
The WWW: lines in the pkg-descr files of these ports where not at the
end of those files and have been missed in prior conversion runs.
Approved by: portmgr (implicit) |
2003.09.21_1
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above  ) |
2003.09.21_1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2003.09.21_1
16 Feb 2014 11:43:07
  |
ehaupt |
Support staging |
2003.09.21_1
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
2003.09.21_1
19 Jun 2013 16:36:53
|
bsam |
. add license (GPLv2);
. bump PORTREVISION;
. trim article from COMMENT;
. trim Makefile headers. |
2003.09.21
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
2003.09.21
03 May 2006 23:26:35
|
edwin |
Remove USE_REINPLACE from all categories starting with B |
2003.09.21
24 Nov 2005 00:04:00
|
pav |
- Add SHA256 |
2003.09.21
12 Mar 2004 13:53:24
|
krion |
- Update to version 2003.09.21
PR: ports/64160
Submitted by: Liam J. Foy <liamfoy@sepulcrum.org> |
2002.03.03
05 Feb 2004 20:38:07
|
trevor |
Use PLIST_FILES.
Reviewed by: marcus |
2002.03.03
27 Jan 2004 20:51:07
|
trevor |
Add SIZE. |
2002.03.03
02 Nov 2003 02:48:09
|
edwin |
ports with possibly unreachable MAINTAINERs
*** addresses that seem to be dead:
PR: ports/58694
Submitted by: Oliver Eikemeier <eikemeier@fillmore-labs.com> |
2002.03.03
21 Feb 2003 11:01:38
|
knu |
De-pkg-comment. |
2002.03.03
04 May 2002 21:45:10
|
kris |
Update to sim4-2002.03.03 to unbreak build.
Noticed by: bento |
25 Jan 2002 13:33:01
|
wjv |
- Update to version of 2001-12-30 |
16 Dec 2001 19:36:48
|
steve |
Update to version 2001.10.12. |
19 Feb 2001 12:32:58
|
jeh |
Update to version 2001-02-06 |
26 Oct 2000 11:19:08
|
jeh |
Update biology/sim4 to 2000.10.19 Maintainership over to FreeBSD bio-porters
mailing list |
08 Oct 2000 00:23:30
|
asami |
Convert category biology to new layout. |
09 Sep 2000 10:37:15
|
kevlo |
Fix checksum |
04 Sep 2000 03:44:04
|
kevlo |
Update to version 2000.08.24 |
27 Jul 2000 15:33:01
|
nbm |
Add sim4, an implementation of the sim4 algorithm for aligning expressed DNA
with genomic sequences |
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