Re: [scipion-users] Two minor issues with release-1.1

[Jose M. de la R. T. <del...@gm...>]

Thanks for the feedback David, I think we need to check this to facilitate
the upgrade to other users.

Cheers,
Jose Miguel

On Thu, Apr 20, 2017 at 9:02 PM, David Belnap <db...@co...>
wrote:

> Pablo,
>
> It seems that the ~/.config/scipion/scipion.conf is not getting updated
> with the new directory names.  I recompiled Scipion release-1.1 (per your
> instructions in another email), deleted all attached packages, and
> installed RELION 2.0.3.  When I tried to run a RELION routine inside
> Scipion, I got an error that the RELION_HOME variable
> in ~/.config/scipion/scipion.conf was not right.  I
> renamed ~/.config/scipion/scipion.conf to ~/.config/scipion/scipion.conf.old
> and ran "./scipion config —update”.  That gave me a
> new ~/.config/scipion/scipion.conf that points to the right RELION
> directory.  I think this should also fix any need to make the link I
> mentioned earlier in this thread.
>
> David
>
>
> On Apr 17, 2017, at 11:12 PM, Pablo Conesa <pc...@cn...> wrote:
>
> Thank you David for the feedback.
>
> On 17/04/17 20:09, David Belnap wrote:
>
> Two minor problems when I installed release-1.1:
>
> 1.  Many packages that I had installed were not recognized when I ran “./scipion install —help”.  Only bsoft 1.9.0, dog picker, and chimera in one of my two installations.  I deleted all packages (by deleting the directories and files in the software/em directory.  Then I reinstalled the packages.  Now, the ones I installed can be seen.
>
>
> Yes you are right, what happens here is that the config (at
> ~/.config/scipion/scipion.conf) points to the new installation paths
> while your previous installation has different folder names.
>
> As an example, and mainly for other in the list.
>
> In Scipion V1.0 path to relion was like <scipion_home>/software/em/relion
> whereas in new version is <scipion_home>/software/em/relion-2.0 (pattern
> is package-version)
>
> I guess you ended up with a new config file (with new pattern -> package-
> version) but your actual folder remain with old names. So renaming the
> folder to the new pattern would have been another way to fix it.
>
> We will think about this because, and at least document the "update"
> process and ideally come up with a smooth "migration" of the config files.
>
> 2. I needed to make the following link to get CTFFIND4 to work in release-1.1 (in directory …/scipion/software/em):
> ctffind4 -> ctffind4-4.1.5/
>
> Same here. links will also work!.
>
> Thanks again for the feedback.
>
> David
>
>
>
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