Michael Dondrup | 30 Jan 17:22 2015
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Re: 3rd party logon Need documentation on Gbrowse session handling

Please keep gmod-gbrowse address posted.

On Jan 30, 2015, at 5:17 PM, Michael Dondrup wrote:

> Hi,
> 
> Why would you store the cookie in a database or file? Cookies are stored by the web-client, and retrieved
via their name, this doesn't depend on by which 
> API (perl or php) the cookie was set. However, if the two applications are on different domains this might
cause problems.
> . If you need session management, you should use CGI ::Session, if you need more control over the cookies
use CGI::cookie,
> 
> hope this helps.
> 
> 
> On Jan 30, 2015, at 3:46 PM, Lishuang Shen wrote:
> 
>> Hello, Michael:
>> 
>> Thank you for the quick help.
>> 
>> After checking and comparison, I think my issue is still in last step of cookie setting, where seems my
cookie was not written. It was not written to the folder I specified. And I don't know if it went into
database. My other functions are essentially same as yours except for that I handle 3rd party logon in PHP.
I will investigate it.
>> 
>> 
>> I am quite just started with direct session and cookie manipulation, and still trying to understand the
how the gbrowse authentication  system working.
(Continue reading)

Ryan Doherty | 30 Jan 17:17 2015

Re: 3rd party logon

Hi Lishuang,

Please write only to the gmod list so others can benefit from any solutions we find.  Thanks.

Let me make sure I understand what you're trying to do.  Can you confirm that following?

1. You have an existing PHP application that uses existing user accounts stored in a database (and both are completely separate from GBrowse)
2. The user logs into your PHP application using an existing form you already supply (also separate from GBrowse)
3. You want the user to be able to visit GBrowse and be automatically logged into GBrowse using a parallel GBrowse account
4. Your PHP application and GBrowse will live on the same server (same domain)- this is very important for cookie sharing!

Can you confirm that all this is true?  If so, then you need to add a custom cookie to your PHP login process and then write code in your PHP application to automate GBrowse login and logout.  The solution we settled on is actually pretty complicated.  Let me know if you would like more details or references to source code.

Ryan


On 01/30/2015 10:32 AM, Lishuang Shen wrote:
P {margin-top:0;margin-bottom:0;}
Dear Ryan Doherty:



http://sourceforge.net/p/gmod/mailman/message/30889992/

Hello:

Regarding the 3rd party logon and automatical activation in gbrowse. I need your  advice.



I am following similar strategy Mike and yours above  for 3rd party login done with PHP. I handled
the information with perl PHP::Session and able to read and validate the PHP generated
session and validated with session information stored in Gbrowse mysql.

I use database to store the user and session information, not using files.
So I am trying to activate my validated session information into Gbrowse.
But stuck here regarding how to set cookie. It will jump to the gbrowse page, but not able to logon.


After checking, I think my issue is still in last step of cookie setting, where seems my cookie was not written to the folder I specified with path() or
to any file in server. And I don't know if it went into database or how to authenticate through database.


I am quite just started with direct session and cookie manipulation, and still trying to understand the how the gbrowse authentication  system working.

Lishuang Shen




Thank you,

Lishuang



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Michael Dondrup | 30 Jan 15:01 2015
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Re: 3rd party logon Need documentation on Gbrowse session handling

Hi Lishuang,

could you have a look at: 
https://github.com/mdondrup/GBrowse/blob/master/cgi-bin/samlPostEpr
and tell me if that helps you. The interaction with the gbrowse api starts at line 45.

To avoid a having to rewrite and use the gbrowse main cgi as
a receiver for the POST message I added another endpoint script. Apart from receiving and
validating the encrypted SAML code it also contains the logic to create a gbrowse user and 
session and to initialize the session and to 'redirect' via java script. Note that we trust the 
SAML authentication in that we will also create a new gbrowse user in the database if there
is not already such an account.

Please let me know if you have any further questions.

Best
Michael

Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway

On Jan 30, 2015, at 2:35 PM, Lishuang Shen wrote:

> Hello:
> 
> Regarding your 3rd party logon. I need your  advice.
> 
> http://sourceforge.net/p/gmod/mailman/message/33295297/
> 
> 
> 
> I am following similar strategyto yours above  for 3rd party login done with PHP. I handled
> the information with perl PHP::session and able to read and validate the PHP generated
> session and validated with session information in Gbrowse mysql.
> 
> I use database to store the user and session information, not using files.
> So I am trying to activate my validated session information into Gbrowse.
> But stuck here regarding how to set cookie. It will jump to the gbrowse page, but not able to logon.
> 
> 
> 
> 
> Thank you,
> 
> Lishuang
> 
> 
> 
> 
> #########################################################
> # I am trying to use directly the part of gbrowse login, for some infoirmation:
> 
>    my $nonce = Bio::Graphics::Browser2::Util->generate_id;
>    my $ip    = CGI::remote_addr(); ## OK for ssl?
>    $session-> set_nonce($nonce,$ip, 1); #set_nonce($nonce,$ip,$remember);
>    $session-> using_openid('false');
> 	my $uploadsid  = $userdb-> get_uploads_id($userid);
> 
>    print STDERR "id= $sessionid_from_user, IP: $ip  $nonce  -- username =", $session->username;
>    print STDERR "\nauthorize_user: $userid, $sessionid_from_user ". $session->id . "  2, 'false'.\n
Logon: $sessionid, $nonce\nuploadsid --" . $uploadsid;
>    $session->flush();
> 
> 	
> 	
> #########################################################
> # here I am following your code:
> 
>      ## now generate the html page that will initialize the session
>      ## start with the session cookie:
> 
>      my $cookie = CGI::Cookie->new(-name => 'gbrowse_sess',
>      -path =>  '/var/www/HBCR/gbrowse2/',
>      -expires => '+1M',
>      -value => $session->id );
> 
>      ## some JSON data is required for calling the java script:
> # user or username in GB? I give both
>       my $result = to_json { userOK  => 1,
>                  sessionid => $sessionid_from_user,
>                  username  => $userid,
>                  message   => 'login ok',
>                 };
>      ## import required javascript functions
>  my $htmlhead = "<script src=\"https://mseqdr.org/gbrowse2/js/login.js\" type=\"text/javascript\"></script>
> <script src=\"https://mseqdr.org/gbrowse2/js/controller.js\" type=\"text/javascript\"></script>\n";
> 
>   print header(-type=>"text/html", -cookie=> $cookie);
>   print start_html(-head=>$htmlhead);
>   print STDERR "Found existing user with ID: $userid / $validated_login_id <br>\n$fullname
$email\n<br> PHP SessionID: $id2 <br>\nGbrowse SessionID:$sessionid_from_user -- $sessionid \n".$session->id;
> 
> print "\n\n<script type=\"text/javascript\">\n";
> print "var p = $result;\n";
> print "login_load_account(\"$myurl\", p);\n";
> print "</script>\n";  
>   print end_html();
> }
> 
> 
> 
> 

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Irwandwiyanto | 30 Jan 08:24 2015
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edit html header footer

how to create header and footer??

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Jie | 29 Jan 19:51 2015
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tmp images not wrote, display error

Hi, all

I installed the latest GBROWSE2 in a readhat server.
Now, every thing goes well, I can visit the yeast demo page, however, no images showed for any track. I checked the APACHE error log, it says:

[Thu Jan 29 13:37:48.886919 2015] [authz_core:error] [pid 15364] [client 10.21.211.40:62422] AH01630: client denied by server configuration: /var/tmp/gbrowse2/images/yeast_
advanced/8661fd84dd1ca3aa0b2ea0ccd4a688d1.png, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/


And I also checked the /var/tmp/gbrowse2/ directory, no files wrote. The read and write privilege seems OK, like:

drwxr-xr-x. 3 apache   apache 19 Jan 29 13:33 gbrowse2


Is there any way to fix this problem?


Jie
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Irwandwiyanto | 28 Jan 05:41 2015
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Sequence not appear on gbrowse_details

I tried running gbrowse2 accordance with the installation instructions ,
gbrowse2 already working on localhost and graph databases have also appeared
, but when trying to view details gene DNA sequence does not appear , is
there any thing wrong in the installation ?? 

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Alexey Morozov | 27 Jan 08:20 2015
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Lock file permissions

Dear colleagues,
what permissions do cgisess.db and cgisess.db.lck really need? I was repairing after some meddling with permissions and made them 777, but this feels a bit too much.

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LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Premanand Achuthan | 26 Jan 18:20 2015
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Mouse hover/mouse click doesn't work for certain tracks

HI

We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi enabled.

We used to link out some of our tracks to external sites (eg: RefSeq) ie when we mouse hover, we display the title with name: start..end and upon clicking the same track, we link out to external site. 

We noticed that this is not working for certain tracks after the upgrade.  In our configuration file, we have defined the feature type:source definition as 'feature = processed_transcript:RefSeq ' and as we also wanted to exclude certain feature types from our search results (ie don't show in the search result if the type is processed_transcript), we have added 'exclude types = processed_transcript' in our database definition file.

Reading through the change logs,  exclude types ([foo:database] exclude types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way the Imagemap is generated was changed, 'time-consuming callbacks are only executed when mouse hovers or clicks on the feature'.

Had a look at the modules/logs and on mouse hover/mouse click the search routines are called correctly, fetches the results, and I guess at the end it was filtering for the features that we have excluded  (at RegionSearch.pm's filter_features routine). So we are not getting any result back and the links doesn't work. We can also restore to original behaviour by setting the "inline imagemap" to true for the tracks that we add 'exclude type' and the links on mouse hover/mouse clink works by doing so.

So my hunch is that call backs failure on mouse hover/mouse click for tracks that have "exclude type" defined in database_definition file is a side effect of the new feature introduced in v2.44. I may be wrong as well. Kindly excuse if so.

Wondering if anyone has had any similar issues and is it possible to have the links working without adding the inline imagemap option (for excluded types)?

Thanks
Prem


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Xiong, Jie | 12 Jan 19:00 2015
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Gbrowse installed, and loaded, but none of the click or drag options works

Hi, all

 

I have installed the Gbrowse2 (Redhat).

The gbrowse yeast database loaded , but I it seems not loaded correctly, none of the click or drag options works.

 

I checked the Apache log file, seems like bellow:

 

[Mon Jan 12 12:46:01.710769 2015] [cgi:error] [pid 45447] [client 10.21.211.40:64616] AH01215: GBROWSE NOTICE: To enable PDF generation, please enter the directory "/usr/sh

are/httpd" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0"

to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://172.20.26.72/gbrowse2/

 

 

no error about the  .css and .js file.

 

When I try to export the sequence using the “Download Decorated Fasta File” option, it didn’t export the sequences correctly, seems like bellow:

 

>chrI:NaN..NaN

 

 

Can anyone tell me how to fix this problem?

 

 

Jie

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Jie | 12 Jan 16:37 2015
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gbrowse install errors

Hi, all

I have installed the gbrowse2 in a redhat server.
Now I can access the test yeast page, but it can not show correctly.

I checked the apache error_log file, like bellow, how can I fix this problem? Thanks.


[Mon Jan 12 10:27:06.332038 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: , referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.332167 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://
[Mon Jan 12 10:27:06.332255 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, ref
[Mon Jan 12 10:27:06.332284 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Error::throw, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_a
dvanced/?name=chrI
[Mon Jan 12 10:27:06.332371 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, re
[Mon Jan 12 10:27:06.332474 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedB
[Mon Jan 12 10:27:06.332569 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm
[Mon Jan 12 10:27:06.332745 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/
[Mon Jan 12 10:27:06.332940 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/p
erl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333070 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio
/DB/SeqFeature/Store/Loader.pm:354, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333195 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB
[Mon Jan 12 10:27:06.333325 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/B
[Mon Jan 12 10:27:06.333433 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeatu
[Mon Jan 12 10:27:06.333566 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl
5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333713 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/pe
rl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333872 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/lo
cal/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm:403, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334016 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib6
4/perl5/Bio/Graphics/Browser2/RegionSearch.pm:301, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334139 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib64/perl5/Bio/Gra
[Mon Jan 12 10:27:06.334263 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib64/perl5/Bio/Gr
[Mon Jan 12 10:27:06.334393 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib64/perl5/
Bio/Graphics/Browser2/Render.pm:1940, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334523 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib64/perl5/B
io/Graphics/Browser2/Render.pm:1930, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334641 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphi
[Mon Jan 12 10:27:06.334699 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: /var/www/cgi-bin/gb2/gbrowse:54, referer: http://172.20.26.72/cgi-bin/
gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334786 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: -----------------------------------------------------------, referer: http://
[Mon Jan 12 10:27:06.438501 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: GBROWSE NOTICE: To enable PDF generation, please enter the directory "/usr/sh
are/httpd" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0"
 to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:07.802577 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: GBROWSE NOTICE: To enable PDF generation, please enter the directory "/usr/sh
are/httpd" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0"
 to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416004 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: , referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membr
ane%20trafficking
[Mon Jan 12 10:27:08.416134 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://
[Mon Jan 12 10:27:08.416222 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, ref
[Mon Jan 12 10:27:08.416252 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Error::throw, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_a
dvanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416338 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, re
[Mon Jan 12 10:27:08.416440 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedB
[Mon Jan 12 10:27:08.416536 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm
[Mon Jan 12 10:27:08.416663 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/
[Mon Jan 12 10:27:08.416830 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/p
erl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416965 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio
[Mon Jan 12 10:27:08.417090 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB
[Mon Jan 12 10:27:08.417246 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/B
[Mon Jan 12 10:27:08.417355 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeatu
[Mon Jan 12 10:27:08.417487 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl
[Mon Jan 12 10:27:08.417625 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/pe
[Mon Jan 12 10:27:08.417769 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataSource::show_summary /usr/local/lib64/per
[Mon Jan 12 10:27:08.417920 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib
64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2268, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418071 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local
/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418220 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/
lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418345 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/
[Mon Jan 12 10:27:08.418475 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/
[Mon Jan 12 10:27:08.418602 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bi
[Mon Jan 12 10:27:08.418729 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Gra
[Mon Jan 12 10:27:08.418852 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphi
[Mon Jan 12 10:27:08.418910 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: /var/www/cgi-bin/gb2/gbrowse:54, referer: http://172.20.26.72/cgi-bin/
gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418984 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: -----------------------------------------------------------, referer: http://
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Asma Mistadi | 3 Jan 11:44 2015
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C code in GBrowse

Hello,

What are the critical functions that is accelerated with C code in GBrowse?

Thanks,
Asma

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