Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 38858 - seq-gen: Sequence-Generator simulation of DNA sequence evolution along phylogenetic trees
Summary: seq-gen: Sequence-Generator simulation of DNA sequence evolution along phylog...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: x86 Linux
: Normal normal (vote)
Assignee: Default Assignee for New Packages
URL: http://tree.bio.ed.ac.uk/software/seq...
Whiteboard: sunrise suggested
Keywords: EBUILD
Depends on:
Blocks:
 
Reported: 2004-01-20 15:58 UTC by Pablo Hess
Modified: 2018-06-07 18:25 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
ebuild for v 1.2.7 of Seq-Gen (Seq-Gen-1.2.7.ebuild,773 bytes, text/plain)
2004-01-20 19:13 UTC, Pablo Hess
Details
digest for v 1.2.7 of Seq-Gen (digest-Seq-Gen-1.2.7,65 bytes, text/plain)
2004-01-20 19:15 UTC, Pablo Hess
Details
Updated (seq-gen-1.3.2.ebuild,898 bytes, text/plain)
2010-09-03 06:03 UTC, dE
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Pablo Hess 2004-01-20 15:58:30 UTC
Sequence-Generator: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Written by Nick Grassly and Andrew Rambaut, at the University of Oxford.

Reproducible: Always
Steps to Reproduce:
1.
2.
3.
Comment 1 Pablo Hess 2004-01-20 16:00:33 UTC
Sorry, ebuild still under development.
Comment 2 Pablo Hess 2004-01-20 19:13:43 UTC
Created attachment 24151 [details]
ebuild for v 1.2.7 of Seq-Gen

This ebuild contains a temporary SRC_URI, as the software's official webpage
redirects us to downloading the MacOS executables instead of the UNIX
source-code.
Comment 3 Pablo Hess 2004-01-20 19:15:57 UTC
Created attachment 24152 [details]
digest for v 1.2.7 of Seq-Gen

I'm not sure if digests should be submitted with the ebuilds. I guess it's no
harm, though.
Comment 4 Jakub Moc (RETIRED) gentoo-dev 2007-09-14 15:38:16 UTC
Last release from 2001, the 'alternative site' gone -> WONTFIX.
Comment 5 Pablo Hess 2007-09-18 17:59:06 UTC
(In reply to comment #4)
> Last release from 2001 the 'alternative site' gone.

This is now Seq-Gen's website:
http://tree.bio.ed.ac.uk/software/seqgen/

And its download URL:
http://tree.bio.ed.ac.uk/download.php?id=41&num=1

-> Please reconsider (sorry if this is not enough reason to reopen the bug, but I really think this software should be in the tree).
Comment 6 Jeffrey Gardner (RETIRED) gentoo-dev 2007-09-19 00:44:16 UTC
Having a website/package that's maintained since 2001 makes all the difference to me. I'll give it a go when I get time...
Comment 7 Jeremy Olexa (darkside) (RETIRED) archtester gentoo-dev Security 2008-12-29 18:53:23 UTC
(this is an automated message based on filtering criteria that matched this bug)

Hello, The Gentoo Team would like to firstly thank you for your ebuild
submission. We also apologize for not being able to accomendate you on a timely
manor. There are simply too many new packages.

Allow me to use this opportunity to introduce you to Gentoo Sunrise. The sunrise
overlay[1] is a overlay for Gentoo which we allow trusted users to commit to and
all users can have ebuilds reviewed by Gentoo devs for entry into the overlay.
So, the sunrise team is suggesting that you look into this and submit your
ebuild to the overlay where even *you* can commit to. =)

Because this is a mass message, we are also asking you to be patient with us. We
anticipate a large number of requests in a short time. 

Thanks,
On behalf of the Gentoo Sunrise Team,
Jeremy.

[1]: http://www.gentoo.org/proj/en/sunrise/
[2]: http://overlays.gentoo.org/proj/sunrise/wiki/SunriseFaq
Comment 8 dE 2010-09-03 06:03:58 UTC
Created attachment 245832 [details]
Updated
Comment 9 Amy Liffey gentoo-dev 2016-04-07 18:32:59 UTC
This bug has made no progress for years. Can we please confirm whether this package is still wanted?

If it isn't, or if there is no response within 30 days, we will close this bug.

Thanks

Amy
Comment 10 Michael 'veremitz' Everitt 2016-04-24 09:09:55 UTC
https://github.com/rambaut/Seq-Gen

v1.3.3 seems to be released and maintained within last year.