gbrowse error

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

gbrowse error

Iti Gupta
Dear sir/mam,
I am having an error while following one of your tutorial: Generic Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.

Thanks and Regards,
Iti Gupta


------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

New Microsoft Office PowerPoint Presentation.pptx (319K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: gbrowse error

Scott Cain
Hi Ita,

Please keep the GBrowse mailing list cc'ed so other people can see and help.

The message about permission denied on /var/lib/gbrowse2/sessions/cgisess.db.lck is definitely a problem.  Check the ownership on the /var/lib/gbrowse2 directory and subdirectories.  It should be owned by the same owner that runs apache, which varies from system to system.  If you're using Ubuntu, I believe the owner should be www-data.  If you find that the sessions directory (or the other directories in the gbrowse2 directory) are not owned by www-data, do this:

  sudo chown -R www-data:www-data /var/lib/gbrowse2

If you're not using Ubuntu, please change the "www-data" parts to the appropriate owner's name.

Scott


On Wed, Apr 22, 2015 at 5:39 AM, Iti Gupta <[hidden email]> wrote:
Hey scott,
i do checked my javascript it was enabled and regarding the error log the errors are as follows: 

[root@localhost httpd]# tail error_log

[Tue Apr 21 22:44:21 2015] [error] [client ::1] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin)

[Tue Apr 21 22:44:21 2015] [error] [client ::1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98.

[Tue Apr 21 22:44:22 2015] [error] [client ::1] CGI::param called in list context from package Bio::Graphics::Browser2::Render line 69, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/local/share/perl5/CGI.pm line 408., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Premature end of script headers: gbrowse, referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/


regards,

Iti gupta


On Tue, Apr 21, 2015 at 9:17 PM, Scott Cain <[hidden email]> wrote:
Hello Iti,

Please make sure that javascript is turned on, as that is what you'd see if it's not.  Also, can you please check the apache error log for messages?  If something is going wrong during the creation of that image, you'd see the message there.

Scott


On Tue, Apr 21, 2015 at 7:22 AM, Iti Gupta <[hidden email]> wrote:
Dear sir/mam,
I am having an error while following one of your tutorial: Generic Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.

Thanks and Regards,
Iti Gupta


------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: gbrowse error

Iti Gupta
Hello sir,
i was trying to install gbrowse again since i was not able to figure out the problem as mentioned by you in the previous mail.
while installing GD i faced the following error. Have checked for the dependencies all were installed. When i was viewing in the root cpan it said GD is already installed and updated to the latest version but it is not showing in the installed modules directory (/root/.cpan/Build) . Kindly revert me back the suitable solution to this ASAP.
 Thanks and Regards,
Iti Gupta


.............................................................................................
cpan install GD
Loading internal null logger. Install Log::Log4perl for logging messages
CPAN: Storable loaded ok (v2.49_01)
Reading '/root/.cpan/Metadata'
  Database was generated on Thu, 30 Apr 2015 05:53:27 GMT
Running install for module 'GD'
CPAN: Digest::SHA loaded ok (v5.95)
CPAN: Compress::Zlib loaded ok (v2.068)
Checksum for /root/.cpan/sources/authors/id/L/LD/LDS/GD-2.56.tar.gz ok
CPAN: File::Temp loaded ok (v0.2304)
CPAN: YAML loaded ok (v1.15)
CPAN: CPAN::Meta::Requirements loaded ok (v2.127)
CPAN: Parse::CPAN::Meta loaded ok (v1.4414)
CPAN: CPAN::Meta loaded ok (v2.150001)
CPAN: Module::CoreList loaded ok (v5.20150214)
CPAN: Module::Build loaded ok (v0.4211)
Configuring L/LD/LDS/GD-2.56.tar.gz with Build.PL
Configuring for libgd version 2.0.34.
Checking for stray libgd header files...none found.

Included Features:          GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF GD_FTCIRCLE VERSION_33
GD library used from:       /usr
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GD' version '2.56'
  LDS/GD-2.56.tar.gz
  /usr/local/bin/perl Build.PL -- OK
Running Build for L/LD/LDS/GD-2.56.tar.gz
Building GD
Extracting Image.pm (with variable substitutions)
cc -I/usr/include -I/usr/local/lib/perl5/5.20.2/x86_64-linux/CORE -DXS_VERSION="2.56" -DVERSION="2.56" -fPIC -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF -DVERSION_33 -DHAVE_UNCLOSEDPOLY -DHAVE_FONTCONFIG -DHAVE_FTCIRCLE -c -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/GD.o lib/GD.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/GD/GD.bs')
cc -shared -O2 -L/usr/local/lib -fstack-protector -o blib/arch/auto/GD/GD.so lib/GD.o -L/usr/lib64 -L/usr/lib64 -L/usr/lib64 -L/usr/lib64 -lXpm -lX11 -ljpeg -lfontconfig -lfreetype -lpng12 -lz -lm -lgd
  LDS/GD-2.56.tar.gz
  ./Build -- OK
Running Build test
t/GD.t ........ 1/11 # Testing using gd2 support.

#   Failed test 'image comparison test 7'
#   at t/GD.t line 249.
# Looks like you failed 1 test of 11.
t/GD.t ........ Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/11 subtests 
t/Polyline.t .. ok   

Test Summary Report
-------------------
t/GD.t      (Wstat: 256 Tests: 11 Failed: 1)
  Failed test:  9
  Non-zero exit status: 1
Files=2, Tests=12,  1 wallclock secs ( 0.02 usr  0.04 sys +  0.13 cusr  0.04 csys =  0.23 CPU)
Result: FAIL
Failed 1/2 test programs. 1/12 subtests failed.
  LDS/GD-2.56.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/GD-2.56.tar.gz


On Wed, Apr 22, 2015 at 7:21 PM, Scott Cain <[hidden email]> wrote:
Hi Ita,

Please keep the GBrowse mailing list cc'ed so other people can see and help.

The message about permission denied on /var/lib/gbrowse2/sessions/cgisess.db.lck is definitely a problem.  Check the ownership on the /var/lib/gbrowse2 directory and subdirectories.  It should be owned by the same owner that runs apache, which varies from system to system.  If you're using Ubuntu, I believe the owner should be www-data.  If you find that the sessions directory (or the other directories in the gbrowse2 directory) are not owned by www-data, do this:

  sudo chown -R www-data:www-data /var/lib/gbrowse2

If you're not using Ubuntu, please change the "www-data" parts to the appropriate owner's name.

Scott


On Wed, Apr 22, 2015 at 5:39 AM, Iti Gupta <[hidden email]> wrote:
Hey scott,
i do checked my javascript it was enabled and regarding the error log the errors are as follows: 

[root@localhost httpd]# tail error_log

[Tue Apr 21 22:44:21 2015] [error] [client ::1] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin)

[Tue Apr 21 22:44:21 2015] [error] [client ::1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98.

[Tue Apr 21 22:44:22 2015] [error] [client ::1] CGI::param called in list context from package Bio::Graphics::Browser2::Render line 69, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/local/share/perl5/CGI.pm line 408., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Premature end of script headers: gbrowse, referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/


regards,

Iti gupta


On Tue, Apr 21, 2015 at 9:17 PM, Scott Cain <[hidden email]> wrote:
Hello Iti,

Please make sure that javascript is turned on, as that is what you'd see if it's not.  Also, can you please check the apache error log for messages?  If something is going wrong during the creation of that image, you'd see the message there.

Scott


On Tue, Apr 21, 2015 at 7:22 AM, Iti Gupta <[hidden email]> wrote:
Dear sir/mam,
I am having an error while following one of your tutorial: Generic Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.

Thanks and Regards,
Iti Gupta


------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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


------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse