Re: Help with gbrowse

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Re: Help with gbrowse

Scott Cain
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
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: Help with gbrowse

Shabari Subramanian
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Help with gbrowse

Scott Cain
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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

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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Re: Help with gbrowse

Shabari Subramanian
Hi Scott,

Thank you for your patience on this. 

I realize my mistake with the link. I had not parsed out the organism name from the Note attribute. I made the changes on this conf file. Please find new conf file attached. 

link            = sub {
                       my $feature = shift;
my $Name=$feature->name();       
my ($NOTE) = $feature->attributes("Note");       
return "https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=".$Note."&searchText=locusName:".$Name;                      
               }

Below is an example of a link that works directly on the browser but does not link to from the gbrowse track.

https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Malus domestica&searchText=locusName:MDP0000293627

The link to phytozome is still being tested, so i only have it on one gene on the test site. Here is a link to that gene being shown on our gbrowse test site. It should be public if not please let me know.


The track you should go to is "Eudicot Gene Families (Phytozome 11)". If you click on it, it goes to localhost page on this locus. 

Thank again for your help and your patience on this.

Best

-shabari





On Mon, Jan 23, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Re: Help with gbrowse

Scott Cain
Hi Shabari,

This is going to sound a little condescending, but since I've done it several times, I thought I'd suggest it: are you sure that the config file you're editing is the one the GBrowse is actually using?  Right now the track that you're having difficulty with is not using the callback at all--it's using the default gbrowse_details link as though there were no "link" attribute in the track config at all.  I'd suggest making some other simple, obvious change, like the name of the organism to see if it changes like you'd expect.  Also, make sure that you're restarting apache for changes if you're using something like fastCGI, which caches config files in memory (preventing it from seeing changes without a restart).  Also check the apache error log for any messages that might indicate a problem with the callback.  You can also add warn statements to the callback that would go out to the error log, though my recollection is that warn messages don't always make it to the error log, so YMMV.

Scott


Scott


On Mon, Jan 23, 2017 at 4:15 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Thank you for your patience on this. 

I realize my mistake with the link. I had not parsed out the organism name from the Note attribute. I made the changes on this conf file. Please find new conf file attached. 

link            = sub {
                       my $feature = shift;
my $Name=$feature->name();       
my ($NOTE) = $feature->attributes("Note");       
return "https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=".$Note."&searchText=locusName:".$Name;                      
               }

Below is an example of a link that works directly on the browser but does not link to from the gbrowse track.

https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Malus domestica&searchText=locusName:MDP0000293627

The link to phytozome is still being tested, so i only have it on one gene on the test site. Here is a link to that gene being shown on our gbrowse test site. It should be public if not please let me know.


The track you should go to is "Eudicot Gene Families (Phytozome 11)". If you click on it, it goes to localhost page on this locus. 

Thank again for your help and your patience on this.

Best

-shabari





On Mon, Jan 23, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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

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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Re: Help with gbrowse

Shabari Subramanian
Not at all. I was questioning my sanity when i first saw this behavior. :)

If you notice the other tracks on the test page i sent do go to the expected links. Also if i modify the link to phytozome for the eudicots track to "phytozome.net" it links out fine. I am quite sure the config file i sent is the one gbrowse is using for the species. I did try restarting httpd. I will check the apache error logs. 



On Tue, Jan 24, 2017 at 8:20 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

This is going to sound a little condescending, but since I've done it several times, I thought I'd suggest it: are you sure that the config file you're editing is the one the GBrowse is actually using?  Right now the track that you're having difficulty with is not using the callback at all--it's using the default gbrowse_details link as though there were no "link" attribute in the track config at all.  I'd suggest making some other simple, obvious change, like the name of the organism to see if it changes like you'd expect.  Also, make sure that you're restarting apache for changes if you're using something like fastCGI, which caches config files in memory (preventing it from seeing changes without a restart).  Also check the apache error log for any messages that might indicate a problem with the callback.  You can also add warn statements to the callback that would go out to the error log, though my recollection is that warn messages don't always make it to the error log, so YMMV.

Scott


Scott


On Mon, Jan 23, 2017 at 4:15 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Thank you for your patience on this. 

I realize my mistake with the link. I had not parsed out the organism name from the Note attribute. I made the changes on this conf file. Please find new conf file attached. 

link            = sub {
                       my $feature = shift;
my $Name=$feature->name();       
my ($NOTE) = $feature->attributes("Note");       
return "https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=".$Note."&searchText=locusName:".$Name;                      
               }

Below is an example of a link that works directly on the browser but does not link to from the gbrowse track.

https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Malus domestica&searchText=locusName:MDP0000293627

The link to phytozome is still being tested, so i only have it on one gene on the test site. Here is a link to that gene being shown on our gbrowse test site. It should be public if not please let me know.


The track you should go to is "Eudicot Gene Families (Phytozome 11)". If you click on it, it goes to localhost page on this locus. 

Thank again for your help and your patience on this.

Best

-shabari





On Mon, Jan 23, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Help with gbrowse

Scott Cain
Another thing I'll do when I'm trying to debug something like this is take the callback that is causing problems and put it in "balloon hover" or "balloon click" so that I can see what is actually getting generated by the callback.  

Also for the truly paranoid, I'll retype the whole think including "link =" in case the lines that are there have hidden control characters that are wrecking things (I have a history of this actually happening to me going back to the mid-80s, so it is somewhat justified :-)  What you describe is actually consistent with this hypothesis, though, since a stray control character on the left hand side of the equals sign would make it look like the "link =" was something else.


On Tue, Jan 24, 2017 at 2:50 PM, Shabari Subramanian <[hidden email]> wrote:
Not at all. I was questioning my sanity when i first saw this behavior. :)

If you notice the other tracks on the test page i sent do go to the expected links. Also if i modify the link to phytozome for the eudicots track to "phytozome.net" it links out fine. I am quite sure the config file i sent is the one gbrowse is using for the species. I did try restarting httpd. I will check the apache error logs. 



On Tue, Jan 24, 2017 at 8:20 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

This is going to sound a little condescending, but since I've done it several times, I thought I'd suggest it: are you sure that the config file you're editing is the one the GBrowse is actually using?  Right now the track that you're having difficulty with is not using the callback at all--it's using the default gbrowse_details link as though there were no "link" attribute in the track config at all.  I'd suggest making some other simple, obvious change, like the name of the organism to see if it changes like you'd expect.  Also, make sure that you're restarting apache for changes if you're using something like fastCGI, which caches config files in memory (preventing it from seeing changes without a restart).  Also check the apache error log for any messages that might indicate a problem with the callback.  You can also add warn statements to the callback that would go out to the error log, though my recollection is that warn messages don't always make it to the error log, so YMMV.

Scott


Scott


On Mon, Jan 23, 2017 at 4:15 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Thank you for your patience on this. 

I realize my mistake with the link. I had not parsed out the organism name from the Note attribute. I made the changes on this conf file. Please find new conf file attached. 

link            = sub {
                       my $feature = shift;
my $Name=$feature->name();       
my ($NOTE) = $feature->attributes("Note");       
return "https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=".$Note."&searchText=locusName:".$Name;                      
               }

Below is an example of a link that works directly on the browser but does not link to from the gbrowse track.

https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Malus domestica&searchText=locusName:MDP0000293627

The link to phytozome is still being tested, so i only have it on one gene on the test site. Here is a link to that gene being shown on our gbrowse test site. It should be public if not please let me know.


The track you should go to is "Eudicot Gene Families (Phytozome 11)". If you click on it, it goes to localhost page on this locus. 

Thank again for your help and your patience on this.

Best

-shabari





On Mon, Jan 23, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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

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Re: Help with gbrowse

Shabari Subramanian
Thanks for your help. I will keep at it.

best

-shabari

On Tue, Jan 24, 2017 at 12:00 PM, Scott Cain <[hidden email]> wrote:
Another thing I'll do when I'm trying to debug something like this is take the callback that is causing problems and put it in "balloon hover" or "balloon click" so that I can see what is actually getting generated by the callback.  

Also for the truly paranoid, I'll retype the whole think including "link =" in case the lines that are there have hidden control characters that are wrecking things (I have a history of this actually happening to me going back to the mid-80s, so it is somewhat justified :-)  What you describe is actually consistent with this hypothesis, though, since a stray control character on the left hand side of the equals sign would make it look like the "link =" was something else.


On Tue, Jan 24, 2017 at 2:50 PM, Shabari Subramanian <[hidden email]> wrote:
Not at all. I was questioning my sanity when i first saw this behavior. :)

If you notice the other tracks on the test page i sent do go to the expected links. Also if i modify the link to phytozome for the eudicots track to "phytozome.net" it links out fine. I am quite sure the config file i sent is the one gbrowse is using for the species. I did try restarting httpd. I will check the apache error logs. 



On Tue, Jan 24, 2017 at 8:20 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

This is going to sound a little condescending, but since I've done it several times, I thought I'd suggest it: are you sure that the config file you're editing is the one the GBrowse is actually using?  Right now the track that you're having difficulty with is not using the callback at all--it's using the default gbrowse_details link as though there were no "link" attribute in the track config at all.  I'd suggest making some other simple, obvious change, like the name of the organism to see if it changes like you'd expect.  Also, make sure that you're restarting apache for changes if you're using something like fastCGI, which caches config files in memory (preventing it from seeing changes without a restart).  Also check the apache error log for any messages that might indicate a problem with the callback.  You can also add warn statements to the callback that would go out to the error log, though my recollection is that warn messages don't always make it to the error log, so YMMV.

Scott


Scott


On Mon, Jan 23, 2017 at 4:15 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Thank you for your patience on this. 

I realize my mistake with the link. I had not parsed out the organism name from the Note attribute. I made the changes on this conf file. Please find new conf file attached. 

link            = sub {
                       my $feature = shift;
my $Name=$feature->name();       
my ($NOTE) = $feature->attributes("Note");       
return "https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=".$Note."&searchText=locusName:".$Name;                      
               }

Below is an example of a link that works directly on the browser but does not link to from the gbrowse track.

https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Malus domestica&searchText=locusName:MDP0000293627

The link to phytozome is still being tested, so i only have it on one gene on the test site. Here is a link to that gene being shown on our gbrowse test site. It should be public if not please let me know.


The track you should go to is "Eudicot Gene Families (Phytozome 11)". If you click on it, it goes to localhost page on this locus. 

Thank again for your help and your patience on this.

Best

-shabari





On Mon, Jan 23, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I was a little confused by your original description of the link problem, which was compounded by the fact that the URL you have in the config looks like it only works for A. thaliana features, but the GFF features don't seem to have any (assuming that's what the Note attribute means).  When I tried to manually build a function URL with the callback you provided, I just got a not found message from Phytozome.

But, all of this is to say that I went back and read your original description of the problem and it doesn't feel like a problem with the GBrowse.  Is it possible that you have something either in your /etc/hosts file or at your institution that is rerouting these requests?  The substituting in localhost for the JGI domain is a little weird.  Do you have a publicly available instance of this I can look at?

Thanks,
Scott


On Mon, Jan 23, 2017 at 2:07 PM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

Apologies for not being clearer. 

Thank you for clarifying how the initial landmark works. I am clear on the behavior now.

Please find attached two files, the config file with the broken link to phytozome and a second file with the gff formatted annotations file for the gbrowse track in question. 

Here is the part of the config file that i added to try to link to phytozome. 

link            = sub {
                       my $feature = shift;
                        my $Name=$feature->name();
                        }

Please let me know if you need more information.

Thanks for your help.

-shabari

On Mon, Jan 23, 2017 at 6:58 AM, Scott Cain <[hidden email]> wrote:
Hi Shabari,

I'm cc'ing the GBrowse mailing list so the discussion can be archived.

About the initial landmark: can you provide a copy of the config file that isn't working? I think I described in an earlier email that the initial landmark only comes into effect when someone is visiting the site who has never been there (since after the first visit, a cookie remembers the last cooridinates visited).  If there is some other problem with the initial landmark please describe the problem more thoroughly.

About the links out: please provide the track configuration that isn't working and a sample of the GFF that should be affected by the configuration.  It's pretty hard to troubleshoot from your description :-)

Thanks,
Scott


On Mon, Jan 23, 2017 at 1:09 AM, Shabari Subramanian <[hidden email]> wrote:
Hi Scott,

I recently joined Phoenix Bioinformatics. I have been working on fixing some bugs on the gbrowse viewer and ran into a wall. Tanya Berardini suggested i reach out to you.

Here are the issues i am tackling:

1. I set the inital landmark on the species conf file in /etc/gbrowse to point to specific chr location. However the landmark field still comes up blank on the gbrowse page for the species. 

2. I am trying to set a link from gbrowse tracks of ortholgous genes to the source phytozome pages spcific to the gene on the track. An example of such a link is https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Athaliana&searchText=locusName:AT1G01040. I set this link within the conf file for the species. However, when i mouse over the track, the link points back to localhost. If i change the link to http://www.phytozome.net, the link works fine. http links on other tracks work fine. None of the other links are https links. Any idea why gbrowse is behaving such.

Thanks for your help.

Best

-shabari



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" 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/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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