Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello,

You were right, its working now.
I tested both with sample data-set and with my own data.

Thank you.

--
Prakhar Gaur


On Tue, 2012-06-05 at 14:42 +0000, Podicheti, Ram wrote:

> No, just set WWW2 to "/var/lib/". Also ensure,  "/var/lib/gbrowse2/databases" is writable for apache. I am sure, it is by default, but just in case. I am hoping this should be it. But, if there are more, don't hesitate notifying me. -Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Tuesday, June 05, 2012 10:06 AM
> To: Podicheti, Ram
> Cc: [hidden email]
> Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Hello,
>
> I checked the path where the Gbrowse2 databases are, "/var/lib/gbrowse2/databases"
> Should I change WWW2 = /var/lib/webgbrowse Though this folder will have to be created first.
>
> Thanking you,
> --
> Prakhar Gaur
>
>
> On Tue, 2012-06-05 at 13:52 +0000, Podicheti, Ram wrote:
> > Prakhar,
> > I am bemused. The WWW2 should be set to the location you provided as "root" at the time of installing GBrowse 2.0. The folder "gbrowse2/databases" will be created in the specified root when you install GBrowse. When you said /var/www/html/gbrowse2/databases/ does not exist, either GBrowse is not installed, or it is installed in a different location. I remember you mentioning GBrowse being already installed and it works.  So, it must be location then. Can you check the location for the GBrowse databases folder? It will also be listed on the GBrowse welcome page. Let me know if you are having issues.
> > Thanks,
> >
> > Ram
> >
> > -----Original Message-----
> > From: Prakhar Gaur [mailto:[hidden email]]
> > Sent: Tuesday, June 05, 2012 9:39 AM
> > To: Podicheti, Ram
> > Cc: [hidden email]
> > Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> >
> > Hello,
> >
> > I checked the folders,
> > /var/www/html/webgbrowse exist as well as, /var/www/html/gbrowse2/
> > But, /var/www/html/webgbrowse/gbrowse2/databases
> > or
> > /var/www/html/gbrowse2/databases/
> > Do not exist.
> >
> > Now after making the changes, to WWW2 the errors are still there.
> > But the path for error changes from
> > "/var/www/html/webgbrowse/gbrowse2/databases/" to "/var/www/html/gbrowse2/databases/"
> > Which basically reflects the changes I just made to the variable WWW2.
> > The new errors are these,
> >
> > ----------------------------------------------------------------------
> > ---------------------------------------------------------------------
> > [Tue Jun 05 18:39:37 2012] [error] [client 192.168.1.18] File does not
> > exist: /var/www/html/favicon.ico
> > [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Could not
> > open
> > database: , referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] -------------
> > EXCEPTION: Bio::Root::Exception -------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] MSG: Couldn't open /var/www/html/gbrowse2/databases/af06240c04f255392f5ccd56f4742bb7:
> > No such file or directory, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Error::throw, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::Loader::load
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::memory::post_init
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::new
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataBase::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataSource::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::run
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18]
> > STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] -----------------------------------------------------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> > 192.168.1.18] Premature end of script headers: gbrowse, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> > f255392f5ccd56f4742bb7
> > ----------------------------------------------------------------------
> > ------------------------------------------------------------------
> >
> > Thanking you,
> > --
> > Prakhar Gaur
> >
> >
> > On Tue, 2012-06-05 at 13:15 +0000, Podicheti, Ram wrote:
> > > My apologies. Strike that previous email and read it this way.
> > >
> > > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> > >
> > >
> > > -----Original Message-----
> > > From: Podicheti, Ram
> > > Sent: Tuesday, June 05, 2012 9:12 AM
> > > To: 'Prakhar Gaur'; [hidden email]
> > > Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> > >
> > > Prakhar,
> > > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> > >
> > > Ram
> > >
> > > -----Original Message-----
> > > From: Prakhar Gaur [mailto:[hidden email]]
> > > Sent: Tuesday, June 05, 2012 3:26 AM
> > > To: [hidden email]
> > > Cc: Podicheti, Ram
> > > Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> > >
> > > Hello,
> > >
> > > I have made sure that none of the errors are due to permission issues.
> > > Also I checked the installation of Gbrowse2 on that system, that is also working fine.
> > >
> > > The apache error-log is,
> > > 1st line, Which database is Apache talking about here?
> > > The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
> > > --------------------------------------------------------------------
> > > --
> > > -------- [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
> > > Could not open
> > > database: , referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] -------------
> > > EXCEPTION: Bio::Root::Exception -------------, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] MSG: Couldn't open
> > > /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b
> > > 33
> > > fb834a: No such file or directory, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Error::throw, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> > > referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::DB::SeqFeature::Store::Loader::load
> > > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::DB::SeqFeature::Store::memory::post_init
> > > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::DB::SeqFeature::Store::new
> > > /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Graphics::Browser2::DataBase::open_database
> > > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Graphics::Browser2::DataSource::open_database
> > > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> > > referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Graphics::Browser2::Render::init_database
> > > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Graphics::Browser2::Render::init
> > > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] STACK:
> > > Bio::Graphics::Browser2::Render::run
> > > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18]
> > > STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] -----------------------------------------------------------, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > > 192.168.1.18] Premature end of script headers: gbrowse, referer:
> > > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > > 50 62436a020e840b33fb834a [Tue Jun 05 12:14:25 2012] [error] [client
> > > 192.168.1.18] File does not
> > > exist: /var/www/html/favicon.ico
> > > -----------------------------------------
> > >
> > > The error log is also attached here.
> > >
> > > Thanking you,
> > > --
> > > Prakhar Gaur
> >
> >
>
>



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