Re: [AMBER] Bug Report

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 21 Nov 2014 05:30:30 -0500

Thanks for the report. I’ve made the change.

There should be some simple workarounds here. The only way you should encounter this problem is if you are setting up a local mirror to a folder where you download all of the updates.

In this case, you can set the mirror using update_amber with a command like

“./update_amber --amber-updates /path/to/amber/updates”

or

“./update_amber --ambertools-updates /path/to/amber/updates”

In this case, there is no need to specify “file:///path/to/amber/updates <file:///path/to/amber/updates>” -- it recognizes local folders just fine.

Alternatively, you can make this fix by hand. I won’t release an update for the script, since the workarounds here are easy and the bug itself is unlikely to affect more people (and the side-effects of an update to update_amber are worse than this bug, IMO.

Thanks again for the report!
Jason

> On Nov 21, 2014, at 2:38 AM, Liu, Hui <hl.zju.edu.cn> wrote:
>
> Hi,
>
> I found a little bug in AMBER14. It makes the update fail when a local directory is specified and the path starts with "file:///".
>
> In amber14/updateutils/repos.py, line 321:
> " self.location = self.location.replace('', 'file://')"
> It should be:
> " self.location = self.location.replace('file://', '')"
>
> Hui Liu
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 21 2014 - 03:00:02 PST
Custom Search