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Re: [Gmod-gbrowse] help regarding gbrowse
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From: Scott C. <sc...@sc...> - 2014-09-23 13:22:38
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Hi Umay,
I'm glad you've gotten it working.
What you're describing with asking for one configuration and getting
another is what happens when there is a problem with the configuration that
you want. I don't see anything obvious with the configuration you pasted
into the email, but my eyes aren't as good a configuration parser as
GBrowse. A few questions:
Do you see anything in the apache error log that indicates that there is a
problem?
Did you add an entry for the new configuration file to
/etc/gbrowse/GBrowse.conf?
Scott
On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <kul...@gm...> wrote:
> Hi
>
> Thank you scott....got GBrowse installed with git clone...
> example database of yeast is also working properly...
>
> but now I have created my own conf file as 114635370.conf in
> etc/gbrowse2/gbrowse.conf folder but when I run
> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
> yeast but not my own file
> why is it so and what can I do for that??
>
>
> my conf file is as follows:
>
> [GENERAL]
> description = motifs of 114635370protein
> db_adaptor = Bio::DB::SeqFeature::Store
> db_args = -adaptor memory
> -dir '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>
>
> plugins = BatchDumper FastaDumper
> gbrowse root = gbrowse
> stylesheet = gbrowse.css
> buttons = images/buttons
> js = js
> tmpimages = tmp
> region segment = 500
> initial landmark = 114635370
> balloon tips = 1
> drag and drop = 1
> cache time = 1
> link = AUTO
> image widths = 450 640 800 1024
> hilite fill = beige
> hilite outline = red
> default width = 800
> default features = 114635370
> max segment = 500
> default segment = 50
> zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
> 200000 500000 1000000
> show sources = 1
> overview bgcolor = lightgrey
> detailed bgcolor = lightgoldenrodyellow
> key bgcolor = beige
> examples = 114635370
> automatic classes = 114635370
>
>
> [protein]
> feature = protein
> glyph = so_transcript
> bgcolor = yellow
> forwardcolor = yellow
> reversecolor = turquoise
> height = 6
> description = 1
> balloon hover width = 350
> balloon hover = sub { my = shift; return join ' ',->notes }
> balloon click width = 450
> balloon click = <table>
> <tr><th rowspan="5" align="left"><br>
> This protein brought to you by <a
> href="http://www.expasy.ch">EXPASY</a>.</th>
> <th bgcolor="cyan">Gene </th>
> </tr>
> <tr align='left'><th><a
> href="/cgi-bin/gbrowse_details/motif?name=">See protein
> details</a></th></tr>
> <tr align='left'><th><a
> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
> NCBI</a></th></tr>
> </table>
>
> key = protein
> [pattern]
> feature = pattern
> glyph = so_transcript
> bgcolor = yellow
> forwardcolor = yellow
> reversecolor = turquoise
> height = 6
> description = 1
> balloon hover width = 350
> balloon hover = sub { my = shift; return join ' ',->notes }
> balloon click width = 450
> balloon click = <table>
> <tr><th rowspan="5" align="left"><br>
> This protein brought to you by <a
> href="http://www.expasy.ch">EXPASY</a>.</th>
> <th bgcolor="cyan">Gene </th>
> </tr>
> <tr align='left'><th><a
> href="/cgi-bin/gbrowse_details/motif?name=">See gene
> details</a></th></tr>
> <tr align='left'><th><a
> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
> Wikipedia about </a></th></tr>
> <tr align='left'><th><a
> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
> </table>
>
> key = pattern
>
>
>
> [profile]
> feature = profile
> glyph = so_transcript
> bgcolor = yellow
> forwardcolor = yellow
> reversecolor = turquoise
> height = 6
> description = 0
> balloon hover width = 350
> balloon hover = sub { my = shift; return join ' ',->notes }
> balloon click width = 450
> balloon click = <table>
> <tr><th rowspan="5" align="left"><br>
> This protein brought to you by <a
> href="http://www.expasy.ch">EXPASY</a>.</th>
> <th bgcolor="cyan">Gene </th>
> </tr>
> <tr align='left'><th><a
> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
> Wikipedia about </a></th></tr>
> <tr align='left'><th><a
> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
> </table>
> key = profile
>
> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <sc...@sc...> wrote:
> > Hi Umay,
> >
> > I don't really know what the problem is--my guess is that there is a
> network
> > problem. Can you try from a different network? Can you clone other
> things
> > from git but just not GBrowse (I would find that pretty strange if it
> were
> > the case)? Also, in case there is a problem with any of the software
> > packages you are using, you should probably run
> >
> > sudo apt-get update
> > sudo apt-get upgrade
> >
> > to make sure your system is up to date.
> >
> > Scott
> >
> >
> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <kul...@gm...>
> wrote:
> >>
> >> Hi
> >>
> >> when I do
> >> git clone https://github.com/GMOD/GBrowse.git
> >>
> >> I get the following error:
> >>
> >> Cloning into 'GBrowse'...
> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
> >> gnutls_handshake() failed: A TLS packet with unexpected length was
> >> received.
> >>
> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <sc...@sc...>
> wrote:
> >> > Hi Umay,
> >> >
> >> > I suspect you are using Ubuntu 14.04 (you may have already told me
> >> > that--I
> >> > don't remember). While working recently on some minor bug fixes for
> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
> >> > dramatically rearranged the file structure for system files, which
> broke
> >> > the
> >> > GBrowse installer. The easiest way to install GBrowse correctly at
> the
> >> > moment is to get a GitHub checkout of the current source and install
> >> > that
> >> > way. It's fairly straight forward; this is what you do:
> >> >
> >> > git clone https://github.com/GMOD/GBrowse.git
> >> > cd GBrowse
> >> > perl Build.PL #accepting the defaults should be fine
> >> > ./Build
> >> > ./Build test
> >> > sudo ./Build install
> >> >
> >> > After doing that you should be able to go to
> http://localhost/gbrowse2
> >> > though the links for sample data sets are written assuming you have
> >> > fastcgi
> >> > installed (which is a good idea to use, because it makes things
> faster),
> >> > but
> >> > if you don't have fastcgi, you should still be able to go to
> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
> If
> >> > that
> >> > works, you should be able to proceed with the tutorial as well.
> >> >
> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <kul...@gm...>
> >> > wrote:
> >> >>
> >> >> whenever we write localhost it looks for files in /var/www/html
> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
> >> >>
> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <kul...@gm...
> >
> >> >> wrote:
> >> >> > The apache error log shows :
> >> >> >
> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
> AH00094:
> >> >> > Command line: '/usr/sbin/apache2'
> >> >> >
> >> >> >
> >> >> > This is the last comment in /var/log/apache2/error.log...... it
> shows
> >> >> > nothing regarding the files not found
> >> >> >
> >> >> >
> >> >> > In the access.log file the last comment is :
> >> >> >
> >> >> >
> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
> >> >> >
> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <sc...@sc...>
> >> >> > wrote:
> >> >> >> Hi Umay,
> >> >> >>
> >> >> >> What does it say in the apache error log? If you're getting a
> >> >> >> message
> >> >> >> about a file not being found, it will record where it was looking
> >> >> >> for the
> >> >> >> file. The error log is in /var/log/apache2. The most recent
> message
> >> >> >> is at
> >> >> >> the end of the file.
> >> >> >>
> >> >> >> Scott
> >> >> >>
> >> >> >>
> >> >> >> Sent from my iPhone
> >> >> >>
> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum <kul...@gm...
> >
> >> >> >>> wrote:
> >> >> >>>
> >> >> >>> hi
> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
> >> >> >>> again
> >> >> >>> its the same the requested url is not found on the server...
> >> >> >>> what should I do??
> >> >> >>> where am I going wrong??
> >> >> >>> can you please tell me how can I start from scratch that is
> >> >> >>> uninstall
> >> >> >>> and then reinstall....
> >> >> >>>
> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <
> sc...@sc...>
> >> >> >>>> wrote:
> >> >> >>>> Umay,
> >> >> >>>>
> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
> >> >> >>>> mailing
> >> >> >>>> list.
> >> >> >>>>
> >> >> >>>> A few things:
> >> >> >>>>
> >> >> >>>> The url you are using is not correct; it should be
> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to
> >> >> >>>> from
> >> >> >>>> http://localhost/gbrowse2/
> >> >> >>>>
> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but only
> >> >> >>>> one
> >> >> >>>> of them
> >> >> >>>> will work. The typical configuration would be for the one in
> >> >> >>>> /var/lib/gbrowse2/databases to work.
> >> >> >>>>
> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
> apache
> >> >> >>>> is
> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it
> >> >> >>>> is
> >> >> >>>> in your
> >> >> >>>> case.
> >> >> >>>>
> >> >> >>>> Scott
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
> >> >> >>>>> <kul...@gm...>
> >> >> >>>>> wrote:
> >> >> >>>>>
> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
> >> >> >>>>>
> >> >> >>>>> I have the following files:
> >> >> >>>>> etc/gbrowse2/GBrowse.conf
> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder
> >> >> >>>>> with
> >> >> >>>>> my own data files
> >> >> >>>>> usr/lib/cgi-bin/gb2
> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
> >> >> >>>>>
> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
> shows
> >> >> >>>>> the
> >> >> >>>>> following url was not found on the server
> >> >> >>>>>
> >> >> >>>>> where is the cgi-bin mentioned in the url located when it is
> not
> >> >> >>>>> in
> >> >> >>>>> /var/www/
> >> >> >>>>>
> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
> >> >> >>>>> <kul...@gm...>
> >> >> >>>>> wrote:
> >> >> >>>>>> Hi
> >> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
> >> >> >>>>>> but when I point my browser to
> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
> following
> >> >> >>>>>> url
> >> >> >>>>>> is
> >> >> >>>>>> not found on this server..
> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it is
> not
> >> >> >>>>>> in
> >> >> >>>>>> /var/www/
> >> >> >>>>>>
> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
> >> >> >>>>>>> <sc...@sc...>
> >> >> >>>>>>> wrote:
> >> >> >>>>>>> Hi Umay,
> >> >> >>>>>>>
> >> >> >>>>>>> Can you please tell us what you done and where you think the
> >> >> >>>>>>> process
> >> >> >>>>>>> has failed? For instance, what do you see when you go to the
> >> >> >>>>>>> built in
> >> >> >>>>>>> sample yeast data set?
> >> >> >>>>>>>
> >> >> >>>>>>> Scott
> >> >> >>>>>>>
> >> >> >>>>>>> Sent from my iPhone
> >> >> >>>>>>>
> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
> >> >> >>>>>>>> <kul...@gm...>
> >> >> >>>>>>>> wrote:
> >> >> >>>>>>>>
> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since a
> month
> >> >> >>>>>>>> but to
> >> >> >>>>>>>> no result....
> >> >> >>>>>>>> can someone help me regarding the installation process.
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> ------------------------------------------------------------------------------
> >> >> >>>>>>>> Want excitement?
> >> >> >>>>>>>> Manually upgrade your production database.
> >> >> >>>>>>>> When you want reliability, choose Perforce
> >> >> >>>>>>>> Perforce version control. Predictably reliable.
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> >> >> >>>>>>>>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> >> >> >>>>>>>> _______________________________________________
> >> >> >>>>>>>> Gmod-gbrowse mailing list
> >> >> >>>>>>>> Gmo...@li...
> >> >> >>>>>>>> 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
> >
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D. scott at scottcain
> dot
> > net
> > GMOD Coordinator (http://gmod.org/) 216-392-3087
> > Ontario Institute for Cancer Research
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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