Different display properties for different objects in the track?

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Different display properties for different objects in the track?

Vladimir Gritsenko
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough. I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
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Re: Different display properties for different objects in the track?

Scott Cain
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 <[hidden email]> wrote:
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough. I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
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hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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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

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Re: Different display properties for different objects in the track?

Vladimir Gritsenko
Hi Scott,

I’m trying to upload a track. I understand there’s a security issue, but there’s 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 I’m 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 <[hidden email]> 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 <[hidden email]> wrote:
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough. I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: Different display properties for different objects in the track?

Scott Cain
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:


Scott



On Fri, Feb 13, 2015 at 10:06 AM, Vladimir Gritsenko <[hidden email]> wrote:
Hi Scott,

I’m trying to upload a track. I understand there’s a security issue, but there’s 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 I’m 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 <[hidden email]> 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 <[hidden email]> wrote:
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough. I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: Different display properties for different objects in the track?

Weeks, Nathan
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

--
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/


--------------------------------------------------------------------------------
From:Scott Cain [[hidden email]]
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<[hidden email]>wrote:

Hi Scott,


I’m trying to upload a track. I understand there’s a security issue, but there’s 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 I’m 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 <[hidden email]> 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<[hidden email]>wrote:
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough.
I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now.http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
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




This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: Different display properties for different objects in the track?

Vladimir Gritsenko
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 you’re right about that.

If the feature is not yet implemented, and there is no alternative solution, I can try and implement Keiran’s suggestion for trusted_remote_url. Is that OK with you?

Finally, I see that there’s no 2.49 tag in github’s GBrowse repo. Makes me wonder how CGD are working with that version.

On Feb 13, 2015, at 17:43, Weeks, Nathan <[hidden email]> 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

--
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/


--------------------------------------------------------------------------------
From:Scott Cain [[hidden email]]
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<[hidden email]>wrote:

Hi Scott,


I’m trying to upload a track. I understand there’s a security issue, but there’s 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 I’m 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 <[hidden email]> 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<[hidden email]>wrote:
Hello all,

I’m working with CGD’s GBrowse (2.49). I want to create a track of SNPs (and for this I’m 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 isn’t good enough.
I tried using Perl callbacks, but this doesn’t seem to work for CGD’s GBrowse instance. Is this possible, and if yes, how?

Thank you in advance,
Vladimir Gritsenko
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now.http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
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




This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


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