Port details |
- tRNAscan-SE Searching for tRNA genes in genomic sequence
- 2.0.11 biology
=2 2.0.11Version of this port present on the latest quarterly branch. - Maintainer: mzaki@e-mail.ne.jp
![search for ports maintained by this maintainer search for ports maintained by this maintainer](/images/search.jpg) - Port Added: 2002-03-27 14:19:04
- Last Update: 2022-10-12 11:45:24
- Commit Hash: 5a4350d
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3+
- WWW:
- http://lowelab.ucsc.edu/tRNAscan-SE/
- Description:
- tRNAscan-SE was written in the PERL (version 5.0) script language.
Input consists of DNA or RNA sequences in FASTA format. tRNA
predictions are output in standard tabular or ACeDB format.
tRNAscan-SE does no tRNA detection itself, but instead combines the
strengths of three independent tRNA prediction programs by negotiating
the flow of information between them, performing a limited amount of
post-processing, and outputting the results in one of several
formats.
¦ ¦ ¦ ¦ ![SVNWeb SVNWeb](/images/subversion.png)
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- tRNAscan-SE>0:biology/tRNAscan-SE
- To install the port:
- cd /usr/ports/biology/tRNAscan-SE/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/tRNAscan-SE
- pkg install tRNAscan-SE
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: tRNAscan-SE
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1665480264
SHA256 (trnascan-se-2.0.11.tar.gz) = 29b74edd0f84ad88139035e119b66397c54a37428e0b61c66a1b3d4733adcd1e
SIZE (trnascan-se-2.0.11.tar.gz) = 4430973
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:
-
- autoconf>=2.71 : devel/autoconf
- automake>=1.16.5 : devel/automake
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Runtime dependencies:
-
- cmsearch : biology/infernal
- 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_tRNAscan-SE
- USES:
- autoreconf perl5
- 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 |
2.0.11 12 Oct 2022 11:45:24
![commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9 commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9](/images/git.png) ![commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9 commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9](/images/codeberg.svg) ![commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9 commit hash: 5a4350de941e061def79fb2ab6b6f46d5eb10ad9](/images/github.svg) ![files touched by this commit files touched by this commit](/images/logs.gif) |
Nuno Teixeira (eduardo) ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) Author: Motomichi Matsuzaki |
biology/tRNAscan-SE: Update to 2.0.11
ChangeLog: http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt
PR: 266966 |
07 Sep 2022 21:58:51
![commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4](/images/git.png) ![commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4](/images/codeberg.svg) ![commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4](/images/github.svg) ![files touched by this commit files touched by this commit](/images/logs.gif) |
Stefan Eßer (se) ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
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) |
2.0.5 07 Sep 2022 21:10:59
![commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52](/images/git.png) ![commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52](/images/codeberg.svg) ![commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52](/images/github.svg) ![files touched by this commit files touched by this commit](/images/logs.gif) |
Stefan Eßer (se) ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
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 ) |
2.0.5 20 Jul 2022 14:20:57
![commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671](/images/git.png) ![commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671](/images/codeberg.svg) ![commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671](/images/github.svg) ![files touched by this commit files touched by this commit](/images/logs.gif) |
Tobias C. Berner (tcberner) ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
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 ) |
2.0.5 06 Apr 2021 14:31:07
![commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb](/images/git.png) ![commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb](/images/codeberg.svg) ![commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb](/images/github.svg) ![files touched by this commit files touched by this commit](/images/logs.gif) |
Mathieu Arnold (mat) ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Remove # $FreeBSD$ from Makefiles. |
2.0.5 13 Jan 2020 17:36:58
![Revision:522898 Revision:522898](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
fernape ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
biology/tRNAscan-SE: update to 2.0.5
This commit also changes maintainer's email.
PR: 243248
Submitted by: mzaki@e-mail.ne.jp (maintainer) |
2.0.3 08 Jun 2019 01:31:19
![Revision:503695 Revision:503695](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
swills ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
biology/tRNAscan-SE: Update to 2.0.3
PR: 238253
Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> |
2.0.0_1 30 May 2019 07:39:07
![Revision:503045 Revision:503045](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
pkubaj ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
biology/tRNAscan-SE: fix build with GCC-based architecturs
Add MAKE_JOBS_UNSAFE=yes to fix build.
Remove USES=compiler:c11, it's not necessary.
PR: 237848
Approved by: mzaki@niid.go.jp (maintainer), linimon (mentor)
Differential Revision: https://reviews.freebsd.org/D20439 |
2.0.0_1 07 May 2019 19:45:17
![Revision:500976 Revision:500976](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
pkubaj ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
biology/tRNAscan-SE: fix build with GCC-based architectures
Add USES=compiler:c11 to fix build.
Approved by: mentors (implicit approval) |
2.0.0_1 28 Sep 2018 00:12:49
![Revision:480837 Revision:480837](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
wen ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
- Unbreak by adding missing pkg-plist
PR: 228758
Submitted by: mzaki@niid.go.jp(maintainer) |
2.0.0_1 29 Jun 2018 12:43:20
![Revision:473544 Revision:473544](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
antoine ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Mark BROKEN: missing plist |
2.0.0 06 Jun 2018 15:20:57
![Revision:471852 Revision:471852](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
krion ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Update to 2.0.0 and pass maintainership to committer.
PR: 228758
Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> |
1.23_1 05 May 2018 10:49:36
![Revision:469100 Revision:469100](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
antoine ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Deprecate ports broken for more than 6 months |
1.23_1 13 Oct 2017 11:14:53
![Revision:451982 Revision:451982](/images/subversion.png) ![Sanity Test Failure Sanity Test Failure](/images/stf.gif) |
bapt ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Mark as broken ports with no public distfiles |
1.23_1 13 May 2016 18:38:34
![Revision:415128 Revision:415128](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
bapt ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Prevent collision with getline(3) |
1.23_1 29 Jul 2014 19:11:53
![Revision:363374 Revision:363374](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
adamw ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...
Approved by: portmgr (not really, but touches unstaged ports) |
1.23_1 05 May 2014 10:26:16
![Revision:352989 Revision:352989](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
bapt ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Support stage |
1.23_1 05 Feb 2014 23:44:50
![Revision:342905 Revision:342905](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
marino ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
biology/tRNAscan-SE: Fix hardcoded perl path |
1.23_1 20 Sep 2013 15:55:44
![Revision:327709 Revision:327709](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
bapt ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
1.23_1 03 Aug 2013 08:45:52
![Revision:324181 Revision:324181](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
az ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
- Convert to new perl framework
- Trim Makefile header |
1.23_1 19 Jun 2013 19:20:26
![Revision:321314 Revision:321314](/images/subversion.png) ![files touched by this commit files touched by this commit](/images/logs.gif) |
bsam ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. pet portlint: use {} instaed of () at variable;
. use PLIST_FILES, PORTDATA and PORTDOCS at Makefile;
. get rid of pkg-plist;
. remove article from COMMENT;
. trim Makefile headers. |
1.23_1 19 Mar 2011 12:38:54
![files touched by this commit files touched by this commit](/images/logs.gif) |
miwi ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
- Get Rid MD5 support |
1.23_1 22 May 2008 00:49:42
![files touched by this commit files touched by this commit](/images/logs.gif) |
miwi ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
- Update MASTER_SITES and WWW: line
- Support CC/CFLAGS properly
- Strip binary
PR: 123866
Submitted by: Ports Fury |
1.23 15 May 2008 02:50:22
![files touched by this commit files touched by this commit](/images/logs.gif) |
erwin ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Update to 1.23 |
1.21 10 Mar 2007 20:20:10
![files touched by this commit files touched by this commit](/images/logs.gif) |
linimon ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Reset chuynh@biolateral.com.au: address bounces.
Hat: portmgr |
1.21 22 Jan 2006 08:20:34
![files touched by this commit files touched by this commit](/images/logs.gif) |
edwin ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
SHA256ify
Approved by: krion@ |
1.21 31 Mar 2004 03:12:58
![files touched by this commit files touched by this commit](/images/logs.gif) |
trevor ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
SIZEify (maintainer timeout) |
1.21 22 Oct 2003 09:29:55
![files touched by this commit files touched by this commit](/images/logs.gif) |
osa ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.
Submitted by: Oleg Karachevtsev <ok@etrust.ru>
A part of PR: 57992 |
1.21 21 Feb 2003 11:01:38
![files touched by this commit files touched by this commit](/images/logs.gif) |
knu ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
De-pkg-comment. |
1.21 04 Nov 2002 01:47:57
![files touched by this commit files touched by this commit](/images/logs.gif) |
edwin ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Port needs perl to build.
Seen on: bento |
1.21 27 Mar 2002 14:18:50
![files touched by this commit files touched by this commit](/images/logs.gif) |
wjv ![search for other commits by this committer search for other commits by this committer](/images/search.jpg) |
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.
PR: 33853
Submitted by: chuynh@biolateral.com.au |