Port details
sim4 Algorithm for aligning expressed DNA with genomic sequences
2003.09.21_1 biology Σ 2003.09.21_1Version of this port present on the latest quarterly branch. 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 11:33:01Last Update: 2024-01-18 18:29:13Commit Hash: b8f4ba2 License: GPLv2WWW: 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 # USE_RC_SUBR (Service Scripts)
no SUBR information found for this port
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 pkg-message: # 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 Muhammad Moinur Rahman (bofh) biology/sim4: Remove expired port
2024-01-17 biology/sim4: Upstream last update was in 2005 2003.09.21_1 Rene Ladan (rene) biology/sim4: fix EXPIRATION_DATE 2003.09.21_1 Muhammad Moinur Rahman (bofh) biology/sim4: Mark DEPRECATED
- Upstream last update was in 2005
- Set EXPIRATION_DATE 2024-01-17 2003.09.21_1 Stefan Eßer (se) Remove WWW lines that have been moved into Makefiles
Approved by: portmgr (implicit) 2003.09.21_1 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 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 Mathieu Arnold (mat) Remove # $FreeBSD$ from Makefiles. 2003.09.21_1 ehaupt Support staging 2003.09.21_1 bapt Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) 2003.09.21_1 bsam . add license (GPLv2);
. bump PORTREVISION;
. trim article from COMMENT;
. trim Makefile headers. 2003.09.21 miwi - Get Rid MD5 support 2003.09.21 edwin Remove USE_REINPLACE from all categories starting with B 2003.09.21 pav - Add SHA256 2003.09.21 krion - Update to version 2003.09.21
PR: ports/64160
Submitted by: Liam J. Foy <liamfoy@sepulcrum.org > 2002.03.03 trevor Use PLIST_FILES.
Reviewed by: marcus 2002.03.03 trevor Add SIZE. 2002.03.03 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 knu De-pkg-comment. 2002.03.03 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
