Hi all,
Scott, I see now that the latest Perl 5 version is 5.20, while Safe::World is supported only in 5.1, so youre right about that.
If the feature is not yet implemented, and there is no alternative solution, I can try and implement Keirans suggestion for trusted_remote_url. Is that OK with you?
Finally, I see that theres no 2.49 tag in githubs GBrowse repo. Makes me wonder how CGD are working with that version.
> On Feb 13, 2015, at 17:43, Weeks, Nathan <***@ars.usda.gov> wrote:
>
> Hi Scott,
>
> I haven't explored this in GBrowse 2. If Keiran doesn't have an immediate
> solution, perhaps this could be added as an issue to the issue tracker?
>
> https://github.com/GMOD/GBrowse/issues <https://github.com/GMOD/GBrowse/issues>
>
> --
> Nathan Weeks
> IT Specialist
> USDA-ARS Corn Insects and Crop Genetics Research Unit
> Crop Genome Informatics Laboratory
> Iowa State University
> http://weeks.public.iastate.edu/ <http://weeks.public.iastate.edu/>
>
>
> --------------------------------------------------------------------------------
> From:Scott Cain [***@scottcain.net]
> Sent:Friday, February 13, 2015 9:33 AM
> To:Vladimir Gritsenko; Keiran Raine; Weeks, Nathan
> Cc:Gbrowse (E-mail)
> Subject:Re: [Gmod-gbrowse] Different display properties for different objects in the track?
>
>
> Hi Vladimir,
>
>
> The last time I looked (which was admitadly a LONG time ago), Safe::World didn't work with any reasonably modern perl; do you know if that's changed?
>
>
> Also, there was some discussion some years back about adding a "trusted remote url" option to GBrowse, but I have a feeling it was never implemented. If Kieran or Nathan would like to comment on it, that would be great:
>
>
> http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/7867
>
>
>
> Scott
>
>
>
>
>
> On Fri, Feb 13, 2015 at 10:06 AM, Vladimir Gritsenko<***@gmail.com>wrote:
>
> Hi Scott,
>
>
> Im trying to upload a track. I understand theres a security issue, but theres also a way to turn on remote calls with Safe::World? Or is that still not considered safe enough?
>
>
> Alternatively, is there a way to have a permanent, server-side configuration file for tracks uploaded from a particular URL (such that any new upload can reference that configuration file)? As Im trying to integrate a different system into CGD, this may
> be a good solution.
>
>
> Thank you!
>
>
>
> On Feb 12, 2015, at 17:54, Scott Cain <***@scottcain.net> wrote:
>
>
> Hi Vladimir,
>
>
> Is this a track of data you are trying to upload or are you doing this in the configuration file? If it's an uploaded track, you can't use perl callbacks in uploaded tracks since that would be a massive security hole to allow random people to execute
> perl on CGD's server.
>
>
> If you're trying to do it in the configuration file, can you please send a sample of the GFF and track configuration that isn't working?
>
>
> Scott
>
>
>
> On Thu, Feb 12, 2015 at 9:23 AM, Vladimir Gritsenko<***@gmail.com>wrote:
> Hello all,
>
> Im working with CGDs GBrowse (2.49). I want to create a track of SNPs (and for this Im using glyph=triangle), where each SNP (triangle) may have one of a predefined list of colours. So, while I can set bgcolor for the entire track, this isnt good enough.
> I tried using Perl callbacks, but this doesnt seem to work for CGDs GBrowse instance. Is this possible, and if yes, how?
>
> Thank you in advance,
> Vladimir Gritsenko
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> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
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