Yes, GBrowse can't figure out what database to use (I started to write that
it can't connect to the database, but that would be the next step that it
didn't even get to yet).
A few things to try:
* use an explicit dsn string, like this: "-dsn dbi:mysql:database=soydb"
The perl mysql adaptor can be pretty forgiving with stuff like that, but
perhaps it's causing a problem.
* try adding an explicit database stanza that looks like this:
[this_database:database]
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=soydb
-user username
-pass password
#search options = default, +wildcard, -stem, +fulltext, +autocomplete
db_adaptor = Bio::DB::SeqFeature::Store
If you do this, it needs to be after everything in the [GENERAL] section.
I usually put it before the track defaults section, and then in the track
defaults, I would add
database = this_database (ie, the name given it in the square brackets
starting the stanza)
If neither of those two things work, I'm not sure what to try next.
Scott
On Mon, Nov 21, 2016 at 1:53 PM, Yasasvy Nanyam <***@siu.edu> wrote:
>
> Scott:
>
>
> I should've posted the error_log before. Here it is, should give you some
idea hopefully.
>
>
> [Mon Nov 21 12:47:09.616590 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:09.617615 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:09.617798 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:09.722254 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:09.722341 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:09.722453 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:09.722500 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $db in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 1063.
> [Mon Nov 21 12:47:09.722556 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $dbid in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm line 131.
> [Mon Nov 21 12:47:09.722623 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $dbid in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm line 141.
> [Mon Nov 21 12:47:09.726366 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:09.728120 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:09.728222 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:09.728281 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $db in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 1063.
> [Mon Nov 21 12:47:10.714740 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:10.714878 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:10.715022 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:10.806018 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:10.806117 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:10.806245 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:10.806292 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $db in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 1063.
> [Mon Nov 21 12:47:10.806337 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $dbid in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm line 131.
> [Mon Nov 21 12:47:10.806379 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $dbid in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm line 141.
> [Mon Nov 21 12:47:10.808146 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:10.811616 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for general at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:10.811705 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
> [Mon Nov 21 12:47:10.811762 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $db in hash element at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 1063.
> [Mon Nov 21 12:47:10.836571 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: which: no inkscape in
(/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin)
> [Mon Nov 21 12:47:10.853592 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value in concatenation (.) or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render/HTML.pm line
183.
> [Mon Nov 21 12:47:10.880093 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:10.880193 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for
plugin:RestrictionAnnotator at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:10.880420 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Use of uninitialized value $symbolic_db_name in join or
string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line
937.
> [Mon Nov 21 12:47:10.880512 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Unknown database defined for
plugin:RestrictionAnnotator at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 943.
> [Mon Nov 21 12:47:10.880656 2016] [cgi:error] [pid 4986] [client
::1:37974] AH01215: Could not open database: Can't call method "new" on an
undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm
line 44.
>
>
> Does this look like an issue with MySQL?
>
>
> --
>
>
> Yash
>
> ________________________________
> From: Scott Cain <***@scottcain.net>
> Sent: Monday, November 21, 2016 12:44:18 PM
> To: Yasasvy Nanyam
>
> Cc: Gbrowse (E-mail); ***@gmod.org
> Subject: Re: Trouble accessing new database in GBrowse
>
> Hi Yash,
>
> Was there anything in the apache error log? The message you're getting
might be due to not being able to find the reference sequence that GBrowse
is looking for, which would be the last reference sequence it looked for.
You can add "?reset=1" to the url to get GBrowse to stop looking for the
last reference sequence and instead look for the initial reference, though
you don't have a configured in the conf you sent a few days ago.
>
> Scott
>
>
> On Mon, Nov 21, 2016 at 1:16 PM, Yasasvy Nanyam <***@siu.edu> wrote:
>>
>> Scott:
>>
>>
>> I get an error at the top of the page - "Can't call method "new" on an
undefined value," and nothing else on the page other than a GBrowse page
with "Browser" "select tracks" tabs with no data being displayed.
>>
>>
>> --
>>
>> Yash
>>
>>
>> ________________________________
>> From: Scott Cain <***@scottcain.net>
>> Sent: Monday, November 21, 2016 11:47:39 AM
>> To: Yasasvy Nanyam
>> Cc: Gbrowse (E-mail); ***@gmod.org
>>
>> Subject: Re: Trouble accessing new database in GBrowse
>>
>> Hi Yash,
>>
>> The apache error log would (hopefully) be more helpful. I'm only
somewhat hopeful, though, as all of the apache codes are either 200 (ok) or
304 (unchanged) except for one: the request for /cgi-bin/gb2/gbrowse/yeast
is 302 (redirect) to /cgi-bin/gb2/gbrowse/soydb/ , which seems like the
right thing to do. What happens when you try to load this page?
>>
>> Scott
>>
>>
>> On Mon, Nov 21, 2016 at 11:04 AM, Yasasvy Nanyam <***@siu.edu> wrote:
>> >
>> > Scott:
>> >
>> >
>> > Sorry, I had a long weekend. I did everything you suggested but no
luck. I am copying the apache access log.
>> >
>> >
>> > ::1 - - [21/Nov/2016:08:32:28 -0600] "OPTIONS * HTTP/1.0" 200 - "-"
"Apache/2.4.6 (CentOS) mod_fcgid/2.3.9 (internal dummy connection)"
>> > ::1 - - [21/Nov/2016:08:32:28 -0600] "OPTIONS * HTTP/1.0" 200 - "-"
"Apache/2.4.6 (CentOS) mod_fcgid/2.3.9 (internal dummy connection)"
>> > ::1 - - [21/Nov/2016:08:32:28 -0600] "OPTIONS * HTTP/1.0" 200 - "-"
"Apache/2.4.6 (CentOS) mod_fcgid/2.3.9 (internal dummy connection)"
>> > ::1 - - [21/Nov/2016:08:32:48 -0600] "GET /gbrowse2/ HTTP/1.1" 304 -
"-" "Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:49 -0600] "GET
/gbrowse2/tutorial/tutorial.css HTTP/1.1" 304 - "http://localhost/gbrowse2/"
"Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:49 -0600] "GET /gbrowse2/gmod_cog.jpeg
HTTP/1.1" 304 - "http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:49 -0600] "GET /favicon.ico HTTP/1.1" 404
209 "-" "Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101
Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:51 -0600] "GET /cgi-bin/gb2/gbrowse/yeast
HTTP/1.1" 302 - "http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:55 -0600] "GET /cgi-bin/gb2/gbrowse/soydb/
HTTP/1.1" 200 23036 "http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET /gbrowse2/css/tracks.css
HTTP/1.1" 304 - "http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0
(X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/css/subtracktable.css HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET /gbrowse2/css/snapshots.css
HTTP/1.1" 304 - "http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0
(X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET /gbrowse2/css/karyotype.css
HTTP/1.1" 304 - "http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0
(X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/css/dropdown/dropdown.css HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/css/dropdown/default_theme.css HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/css/titlebar-default.css HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/css/gbrowse_warm.css HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET /gbrowse2/js/prototype.js
HTTP/1.1" 304 - "http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0
(X11; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/js/scriptaculous.js HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET
/gbrowse2/js/subtracktable.js HTTP/1.1" 304 - "
http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> > ::1 - - [21/Nov/2016:08:32:57 -0600] "GET /gbrowse2/js/login.js
HTTP/1.1" 304 - "http://localhost/cgi-bin/gb2/gbrowse/soydb/" "Mozilla/5.0
(X11; Linux x86_64; rv:45.0) Gecko/20100101 Fi
>> >
>> >
>> > Thanks for all you help so far.
>> >
>> >
>> > Regards,
>> >
>> >
>> > Yash
>> >
>> > ________________________________
>> > From: Scott Cain <***@scottcain.net>
>> > Sent: Friday, November 18, 2016 10:23:00 AM
>> > To: Yasasvy Nanyam; Gbrowse (E-mail)
>> >
>> > Cc: ***@gmod.org
>> > Subject: Re: Trouble accessing new database in GBrowse
>> >
>> > Hi Yash,
>> >
>> > I'm cc'ing the GBrowse mailing list; I didn't noticed that it wasn't
cc'ed before.
>> >
>> > I don't see anything obviously wrong with your config files, though I
would suggest as a debugging step that you comment out the [yeast] section
in GBrowse.conf so it doesn't have anything to fall back on when if it
fails trying to get to your database. Also, I'd throw a carriage return at
the end of the GBrowse.conf so that the file doesn't EOF on the same line
as the path for your database (I really don't think that should matter, but
I've been wrong before).
>> >
>> > After you've done those things, take a look at your apache error.log
and show us error messages that might help.
>> >
>> > Scott
>> >
>> >
>> > On Thu, Nov 17, 2016 at 2:29 PM, Yasasvy Nanyam <***@siu.edu>
wrote:
>> >>
>> >> Soctt:
>> >>
>> >>
>> >> I didn't make any config changes to Apache, similar to other systems
where I installed GBrowse before.
>> >>
>> >>
>> >> I am attaching the config files you requested.
>> >>
>> >>
>> >> Regards,
>> >>
>> >>
>> >> Yash
>> >>
>> >> ________________________________
>> >> From: Scott Cain <***@scottcain.net>
>> >> Sent: Thursday, November 17, 2016 12:05:38 PM
>> >> To: Yasasvy Nanyam
>> >> Cc: ***@gmod.org
>> >> Subject: Re: Trouble accessing new database in GBrowse
>> >>
>> >> Hi Yasasvy,
>> >>
>> >> Is the reference to the yeast URL a referrer? I'm not sure how your
apache log is configured, but that occurred to me as a possibility.
>> >>
>> >> In any event, it is probably a config file problem. Can you send you
GBrowse.conf and species specific config?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Thu, Nov 17, 2016 at 12:33 PM, Yasasvy Nanyam <***@siu.edu>
wrote:
>> >>>
>> >>> Dear GMOD team:
>> >>>
>> >>>
>> >>> I've created and added a new database but I cannot access it from
GBrowse. I've done this before without any issues, but this time there
seems to be a problem for which I don't have a solution.
>> >>>
>> >>>
>> >>> I've created a database "soydb" and created a config file and loaded
the sequences using "bp_seqfeature_load.pl" tool. But I cannot access the
data. I've checked the Apache log and this is what I got:
>> >>>
>> >>>
>> >>> ::1 - - [17/Nov/2016:11:21:09 -0600] "GET
/cgi-bin/gb2/gbrowse/soydb/ HTTP/1.1" 200 23212 "
http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11; Linux
x86_64; rv:45.0) Gecko/20100101 Firefox/45.0"
>> >>>
>> >>>
>> >>> I don't know why it is trying to access the example yeast database
when I am trying to access soydb. Is there a possible solution?
>> >>>
>> >>>
>> >>> Thanks,
>> >>>
>> >>>
>> >>> Yasasvy Nanyam
>> >>>
>> >>> Graduate Assistant, IT Research
>> >>>
>> >>> SIUC
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >>
------------------------------------------------------------------------
>> >> 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
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research