Alexey Morozov | 27 Aug 09:52 2014
Picon

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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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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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
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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
------------------------------------------------------------------------------
Prabha Karan | 11 Aug 13:56 2014
Picon

reg: GBrowse 2.0

hi,
    i am configured gbrowse in my local server. i want to change the user interface of gbrowse. is that possible to change main html file to our style.please help me
i want to remove file,help tabs, scroll/zoom.........

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navillusol | 11 Aug 18:28 2014
Picon

Not Found

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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navillusol | 5 Aug 18:56 2014
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Re: Invoking gbrowse

Hey Scott, ya bit mess! I was going to just sudo apt-get purge gbrowse :

 that will get rid of the original gbrowse that was on the machine, in theory leaving only gbrowse2. Does that seem correct to you?


On Tue, Aug 5, 2014 at 5:45 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

Can we back up several steps?  You're using BioLinux 12.04, right?  That comes with GBrowse 2.38 already installed.  Did you then install another version of GBrowse2 on top of that?  Ugh.  That's a mess.  How attached are you to this instance of Biolinux?  If it's a vm or AWS instance, it might be easier for you to pitch it and start over.

It's fairly easy to remove the gbrowse installed by apt-get and install a newer version, but it requires a few commands.

Scott



On Tue, Aug 5, 2014 at 10:26 AM, navillusol <[hidden email]> wrote:
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data' <at> localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Scott Cain | 5 Aug 18:54 2014
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Re: Invoking gbrowse

If you are attached to your instance, you could try this:

  sudo apt-get remove --purge gbrowse

however, this may also remove several packages that GBrowse depends on, which will be a hassle but not insurmountable.  This command will remove the gbrowse files that were installed from the debian package.  Then you may have to reinstall GBrowse2 on the command line to replace anything the it needs that apt-get may have removed.

Scott



On Tue, Aug 5, 2014 at 12:45 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Liam,

Can we back up several steps?  You're using BioLinux 12.04, right?  That comes with GBrowse 2.38 already installed.  Did you then install another version of GBrowse2 on top of that?  Ugh.  That's a mess.  How attached are you to this instance of Biolinux?  If it's a vm or AWS instance, it might be easier for you to pitch it and start over.

It's fairly easy to remove the gbrowse installed by apt-get and install a newer version, but it requires a few commands.

Scott



On Tue, Aug 5, 2014 at 10:26 AM, navillusol <navillusol858-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data' <at> localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Scott Cain | 4 Aug 20:41 2014
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Re: Invoking gbrowse

Hi Liam,

Would be reluctant to say anything definitely :-)

The fact that there are no errors in the apache log makes me think you're not looking in the right log file.  Apache can be configured to use more than one log file, so it's possible that the GBrowse logs are going elsewhere.  Did you install this instance of GBrowse or did it come with biolinux?

Also, is there an images directory in /var/tmp/gbrowse2, and is there anything in that directory?

Scott



On Mon, Aug 4, 2014 at 11:52 AM, Liam O'Sullivan <navillusol858 <at> gmail.com> wrote:
Yes that is the directory set for tmp_base in the .conf file, nope no errors regarding 404/file not found. So it definitely isn't a permission issue? 


On Mon, Aug 4, 2014 at 4:08 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
OK, good, so the directory exists and has appropriate permissions.  Is that what directory is set for tmp_base in GBrowse.conf?  What about your apache error log?  Are there any 404/file not found messages in it?


On Mon, Aug 4, 2014 at 9:56 AM, navillusol <navillusol858-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research




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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research
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