Menu
▾
▴
gmod-gbrowse
|
From: Scott C. <sc...@sc...> - 2022-04-30 00:03:38
|
Hi Kiran, Oh, that could be difficult to debug. I'll start with suggesting that you move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new features getting added often). http://jbrowse.org/ I'll start with this: is the mysql database on the same machine as the GBrowse 2 install, and are there any useful error messages in the apache error log? Are the DBI and DBD::mysql perl modules installed? Scott On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > Hi, > > > > I have question about gbrowse2 that we have setup on a new server since we > migrated. We have setup everything however the gbrowse is not able to call > the MySQL database. How can I check what is missing to make the connection > successfully? > > > > Thanks! > > Kiran > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
|
From: Scott C. <sc...@sc...> - 2022-04-30 00:17:43
|
Are there any error messages in the apache error log? The connection bit I use in my (very old but still mostly functional) GBrowse instance looks like this: [this_database:database] db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=c_elegans_PRJNA13758_WS284;host=rdbms.wormbase.org -user ********* -pass ********* search options = default, +wildcard, -stem, +fulltext, +autocomplete db_adaptor = Bio::DB::SeqFeature::Store On Fri, Apr 29, 2022 at 4:34 PM Rajaya, Kiran <ra...@bc...> wrote: > Hi Scott, > > Thanks for your prompt response. The MySQL is on a different server from > where gbrowse is installed and we are able to connect to MySQL fine.. the > modules are also installed. > > Thanks > Kiran > > Get Outlook for Android <https://aka.ms/AAb9ysg> > > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022, 6:10 PM > *To:* Rajaya, Kiran <ra...@bc...>; Gbrowse (E-mail) < > gmo...@li...> > *Cc:* he...@gm... <he...@gm...> > *Subject:* Re: gbrowse2 > > ****CAUTION:*** This email is not from a BCM Source. Only click links or > open attachments you know are safe.* > ------------------------------ > Hi Kiran, > > Oh, that could be difficult to debug. I'll start with suggesting that you > move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new > features getting added often). http://jbrowse.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XIIakvN9-mX88hFwKeTtLHUhV8huao67UvIqVIjAhFw&e=> > > I'll start with this: is the mysql database on the same machine as the > GBrowse 2 install, and are there any useful error messages in the apache > error log? Are the DBI and DBD::mysql perl modules installed? > > Scott > > > On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > >> Hi, >> >> >> >> I have question about gbrowse2 that we have setup on a new server since >> we migrated. We have setup everything however the gbrowse is not able to >> call the MySQL database. How can I check what is missing to make the >> connection successfully? >> >> >> >> Thanks! >> >> Kiran >> >> >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=Fd7Ky6SNhoDPhG4W0EMV0GiQqIxTaqUUWyAPj3KKnWc&e=>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=3bxGb8tS10UMCojT16HmKRLk9ZNxLEkDS8F-lunME1M&e=> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XEjtgIqbuOa3aOLXCCijqCTM5oWJre1NDL7EaUr7dac&e=> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=OFzE21Mf6PYkwslGeuMB4xVIDe6lbOf1x4NBbzPM9ac&e=> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=1ayszIll2pyNbqyHxWAiKA0HbnrlueykEKFeA-UiPbA&e=> > ) > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
|
From: Scott C. <sc...@sc...> - 2022-05-02 03:12:39
|
Is this the problem? If so, that should be an easy fix: couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck' Is /var/lib/gbrowse2/sessions/ writable by the webserver? On Fri, Apr 29, 2022 at 5:53 PM Ramanathan, Vivek <vra...@bc...> wrote: > Dear Scott, > > > > Please find attached the error. The error is related to database > connection. > > > > However, the following perl script is successful. > > > > use Bio::DB::SeqFeature::Store; > > > > # Open the feature database > > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > > -dsn => > 'dbi:mysql:database=getbac:host=10.15.12.121', > > -user => 'admin', > > -pass => '######', > > -create => 1 ); > > my $feature = $db->fetch(1); > > > > Regards, > > Vivek > > Ld. Programmer/Analyst > > Tel: (713)798-3425 > > Email: viv...@bc... > > > > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022 7:17 PM > *To:* Rajaya, Kiran <ra...@bc...> > *Cc:* Gbrowse (E-mail) <gmo...@li...>; Ramanathan, > Vivek <vra...@bc...> > *Subject:* Re: gbrowse2 > > > > Are there any error messages in the apache error log? > > > > The connection bit I use in my (very old but still mostly functional) > GBrowse instance looks like this: > > > > [this_database:database] > db_args = -adaptor DBI::mysql -dsn > dbi:mysql:database=c_elegans_PRJNA13758_WS284;host=rdbms.wormbase.org > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rdbms.wormbase.org&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=LHC17xN_My2KVQONxnlYxmectFk9WVzLmlZW64VjKYQ&e=> > -user ********* -pass ********* > search options = default, +wildcard, -stem, +fulltext, +autocomplete > db_adaptor = Bio::DB::SeqFeature::Store > > > > On Fri, Apr 29, 2022 at 4:34 PM Rajaya, Kiran <ra...@bc...> wrote: > > Hi Scott, > > > > Thanks for your prompt response. The MySQL is on a different server from > where gbrowse is installed and we are able to connect to MySQL fine.. the > modules are also installed. > > > > Thanks > > Kiran > > > > Get Outlook for Android > <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_AAb9ysg&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=mw0V_shH7h63pSC23qfNsWoNmgN5VAKZ3Sc1Leuts0g&e=> > > > ------------------------------ > > *From:* Scott Cain <sc...@sc...> > *Sent:* Friday, April 29, 2022, 6:10 PM > *To:* Rajaya, Kiran <ra...@bc...>; Gbrowse (E-mail) < > gmo...@li...> > *Cc:* he...@gm... <he...@gm...> > *Subject:* Re: gbrowse2 > > > ****CAUTION:*** This email is not from a BCM Source. Only click links or > open attachments you know are safe.* > ------------------------------ > > Hi Kiran, > > > > Oh, that could be difficult to debug. I'll start with suggesting that you > move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new > features getting added often). http://jbrowse.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XIIakvN9-mX88hFwKeTtLHUhV8huao67UvIqVIjAhFw&e=> > > > > I'll start with this: is the mysql database on the same machine as the > GBrowse 2 install, and are there any useful error messages in the apache > error log? Are the DBI and DBD::mysql perl modules installed? > > > > Scott > > > > > > On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote: > > Hi, > > > > I have question about gbrowse2 that we have setup on a new server since we > migrated. We have setup everything however the gbrowse is not able to call > the MySQL database. How can I check what is missing to make the connection > successfully? > > > > Thanks! > > Kiran > > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=Fd7Ky6SNhoDPhG4W0EMV0GiQqIxTaqUUWyAPj3KKnWc&e=>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=3bxGb8tS10UMCojT16HmKRLk9ZNxLEkDS8F-lunME1M&e=> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XEjtgIqbuOa3aOLXCCijqCTM5oWJre1NDL7EaUr7dac&e=> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=OFzE21Mf6PYkwslGeuMB4xVIDe6lbOf1x4NBbzPM9ac&e=> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=1ayszIll2pyNbqyHxWAiKA0HbnrlueykEKFeA-UiPbA&e=> > ) > > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=TW7Hj8SS8mCneGx_CFTqFQivwBbGmjvIKLqwjsrL9GI&e=>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wormbase.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=wiaQuEfR1v1uDhNJ3TPkDYecAg8jzTyIfYVgEnsJ6Gg&e=> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alliancegenome.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=JXDGR9JmkcD1Qyoy9iP5uTVmSW9AjfutDXv53wfuSAo&e=> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__virusseq-2Ddataportal.ca_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=Y4lebneF5AwIByya3ycP4dUOJAXY3i7j6jDCWZXNW4M&e=> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__hcmi-2Dsearchable-2Dcatalog.nci.nih.gov_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Aw-d35oMueWL9ZC1DtA2jkstG2_G9UsPtujet09dtPs&m=O-6Tgm2jV9nwizZugYpYb_UXlL3P1i0RKBBGOSMiWTwzBZSROz3h80PTtj7xLSCj&s=OmbzSF4xyLYQEkogmVVC_ZcfV6Iy_IkadGvHiW8FNkQ&e=> > ) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
Thanks for helping keep SourceForge clean.
X