Scott Cain | 17 Sep 16:17 2014
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Re: help regarding gbrowse

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 <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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 <kulsum.umay <at> gmail.com> 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 <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> 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 <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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.
>>>
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umay kulsum | 12 Sep 05:41 2014
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help regarding gbrowse

I have been trying to install and invoke GBrowse since a month but to
no result....
can someone help me regarding the installation process.

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Seth Munholland | 11 Sep 22:25 2014
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Missing Details panel in GBrowseSyn

Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755
Attachment (OAC_Rex_PChr08.synconf): application/octet-stream, 2001 bytes
Attachment (OAC_Rex_PChr08_synteny.conf): application/octet-stream, 944 bytes
Attachment (P.acutifolius_synteny.conf): application/octet-stream, 932 bytes
Attachment (OAC_Rex_PChr08.gff3): application/octet-stream, 1017 bytes
Attachment (P.acutifolius.gff3): application/octet-stream, 397 bytes
Attachment (corrected_Pseu_Pacu_Chr08_matches2.clw): application/octet-stream, 6107 bytes
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Ellen Schofield | 8 Sep 13:17 2014
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Search options in GBrowse (none)

Hi All,

We have recently hit an issue in searching in our version of GBrowse (2.35).  According to the online docs, there is the ability to turn searching off on a specific database using the search:none flag...
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Database_Search_Options

We have done this on some of our larger databases that produce xy scatter plots as searching isn't needed.  However, it would appear that by loading in gff using the Name attribute, that searching is still done, even with "none" set on all databases.  This is slightly counter-intuitive to myself.  I would expect that using the none, which is used to " Disable all searching on this database" should do just this?

I have tracked the issue down to a few lines of code in Bio::Graphics::Browser2::Region (lines 247-251)
https://github.com/GMOD/GBrowse/blob/master/lib/Bio/Graphics/Browser2/Region.pm

Firstly, can I confirm that what I am seeing is the expected behaviours, ie setting search:none on a db still allows searching on feature names in that db?
Secondly, if no, can I suggest that this portion of code is removed to reduce the confusion of "incorrect" results?

I look forward to hearing from you.

Yours,
Ellen.
-- ellen.schofield-piTOwl1TIVXQzY9nttDBhA@public.gmane.org JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, WT/MRC Bldg, Addenbrooke's Hospital, Hills Rd., Cambridge CB2 0XY UK Tel: 01223 763215
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Josh Goodman | 28 Aug 20:34 2014
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Can you cross GBrowse link streams?

Hi all,

A user has reported an issue with following links from a BLAST report
to GBrowse.  The links they are following use standard parameters to
position the view (ref, start, stop).  The links look something like
this:

Link/Tab 1:
http://flybase.org/cgi-bin/gbrowse2/dmel/?ref=2R;start=14479585;stop=14483603;

Link/Tab 2:
http://flybase.org/cgi-bin/gbrowse2/dmel/?ref=2L;start=15260611;stop=15264625;

After opening the above links in their own tab and in quick succession
so that Tab 1 is still loading when Tab 2 initiates a request, the
view shown in Tab 1 is corrupted.  Tab 1 shows the correct URL in the
browser address bar, but the region shown corresponds to the region
for Tab 2.  The tab title and the GBrowse region title also display
the incorrect region.

e.g.
' D. melanogaster: 4.015 kbp from 2L:15,260,611..15,264,625

instead of

' D. melanogaster: 4.019 kbp from 2R:14,479,585..14,483,603

Reloading Tab 1 corrects the corrupted view.  If you click each link
after waiting for the tab to load it does not exhibit this behavior.

I've replicated this on the WormBase GBrowse 2.x server using the
links below, so I'm fairly certain that this is not specific to the
FlyBase installation.

http://www.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/?ref=III&start=9050076..9061680

http://www.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/?ref=III&start=8060076..8071680

Have others seen this?  I know that we are never supposed to cross the
streams, but would it be possible to fix this bug or find a way around
it so that we can?

Thanks,
Josh

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Alexey Morozov | 27 Aug 09:52 2014
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Get scaffold name

Dear colleagues,
how do I programmatically get a name of the scaffold my feature is on? I'm writing a bubble click sub and it goes like this:

balloon click = sub
        {
        my $feature=shift;
        my $text=$feature->name.'<br>';
        $text.='<a href=/gb2/gbrowse/subset/?q=scaffold00001:'.$feature->start.'..'.$feature->end.'>Zoom to feature</a><br><a href=/IPS/'.$feature->name.'-mRNA-1.html>IPS results</a><br>';
        return $text;
        }


I want to replace currently hardcoded 'scaffold00001' to something that will give me an actual scaffold name.
$feature->location->seq_id doesn't work.

And expanding the question, is the API available from inside *.conf files described somewhere? Like, what modules are loaded, what varibles are available and so on.
--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Scott Cain | 27 Aug 01:23 2014
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Both WebApollo and JBrowse are hiring

Both WebApollo and JBrowse are hiring developers in beautiful Berkeley.  Both of these projects are high profile in the bioinformatics community and make use of leading edge technologies.  If you or anyone you know would be interested, please be take a look at these announcements:

WebApollo:

JBrowse:

Scott



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Scott Cain | 14 Aug 18:21 2014
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Re: Not Found

Hi Liam,

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <navillusol858-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <navillusol858 <at> gmail.com> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






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Ontario Institute for Cancer Research




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Scott Cain | 14 Aug 14:26 2014
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Re: help regarding gbrowse

Hi Umay,

The email address is gmod-gbrowse-5NWGOfrQmndRYHbF4JBHZw@public.gmane.orgge.net, and you get a moderation message because you have to be subscribed to the list in order to send messages to it without moderation.  I have always allowed your messages onto the list; the moderation is to keep spammers out.

A few things:

1. The url you are trying (http://localhost/gbrowse2/yeast) won't get you a GBrowse page unless you've done something unusual with your apache config.  A more typical URL would be http://localhost/cgi-bin/gb2/gbrowse/yeast

2. What OS are you using? The apache error log segment makes me think Centos or Fedora but the path to the cgi you originally posted makes me think Debian or Ubuntu. 

3. While you weren't using the correct URL to access GBrowse, the file permissions error in the error log has me worried that something went wrong during the installation, as it should set the permissions correctly.  Do you recall any messages about problems during the installation?

Scott



On Thu, Aug 14, 2014 at 12:02 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Scott
when I mail my question to gmod-gbrowse-bounces-5NWGOfrQmneRv+LV9MX5uvxACJCWSL8g@public.gmane.org I
get the following:
Your message to Gmod-gbrowse awaits moderator approval

Yes I have apache installed and running and the error log shows
"Permission denied: [client 127.0.0.1:46351] AH00132: file permissions
deny server access: /var/www/html/gbrowse/gmod_cog.jpeg, referer:
http://localhost/gbrowse/" when I try http://localhost/gbrowse2/yeast.

Regards
Umay Kulsum
PhD student
AIIMS

On Tue, Aug 12, 2014 at 6:13 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
> Hi Umay,
>
> Please always ask questions like this on the GBrowse mailing list (cc'ed
> here).
>
> Do you have apache installed and running?  What is in the apache error log
> (probably in /var/log/apache2/error_log)?
>
> Scott
>
>
>
> On Tue, Aug 12, 2014 at 1:45 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>>
>> hello Scott,
>>
>> I have installed gbrowse2 via CPAN shell using the command in ubuntu
>> 14.04:
>>
>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>
>> but the example file of yeast not working with the url
>> http://localhost/gbrowse2/yeast
>> it shows the error the rquested url was not found on this server.
>>
>> all the files are installed at default locations such as:
>> /usr/lib/cgi-bin/gb2/gbrowse
>> /etc/gbrowse2/GBrowse.conf
>>
>> but nothing is found in /var/tmp/gbrowse2
>>
>> Can you please help in solving this.
>>
>> Regards
>>
>> Umay Kulsum
>> PhD Student
>> AIIMS
>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Scott Cain | 12 Aug 14:43 2014
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Re: help regarding gbrowse

Hi Umay,

Please always ask questions like this on the GBrowse mailing list (cc'ed here).

Do you have apache installed and running?  What is in the apache error log (probably in /var/log/apache2/error_log)?

Scott



On Tue, Aug 12, 2014 at 1:45 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
hello Scott,

I have installed gbrowse2 via CPAN shell using the command in ubuntu 14.04:

sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'

but the example file of yeast not working with the url
http://localhost/gbrowse2/yeast
it shows the error the rquested url was not found on this server.

all the files are installed at default locations such as:
/usr/lib/cgi-bin/gb2/gbrowse
/etc/gbrowse2/GBrowse.conf

but nothing is found in /var/tmp/gbrowse2

Can you please help in solving this.

Regards

Umay Kulsum
PhD Student
AIIMS



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Samy Jeevan Karloss Antony | 12 Aug 10:59 2014
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Seq Download by feature (only exons, introns)

Hei, 

I have installed GBrowse. 

I want to add an option to GBrowse where users can download only “exons” or “introns” or mRNA
sequence of a gene/regions.  

Is there any Add-ons already to fix this? or any other solutions?  

Thanks,
Jeevan
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