Hong Wang | 2 Jul 16:27 2015
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tutorial on the website

Hi,

 

I am a scientist at Eli Lilly. I am interested in using the website. Do you offer tutorials?

 

Thanks!

 

Hong

 

Hong Wang, Ph.D.

Sr. Research Scientist

Tailored Therapeutics Neuroscience

Eli Lilly and Company

Lilly Corporate Center, Indianapolis, IN 46285, U.S.A.

317-433-2879 (office)

Wang_hong2-hG+hP7PK2UgAvxtiuMwx3w@public.gmane.org |www. Lilly.com

 

CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message

 

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Wiese, Matthew B. | 25 Jun 07:29 2015
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Set up GBrowse to compare the genes of n number of isolates

GBrowse Team,


I'm setting up a GBrowse system for my lab's particular data on fungi.


The researchers would like to use GBrowse to compare the gene differences between two or more isolates.


I've looked through the wiki and have tried web searches but nothing has come up.


Is it possible to modify GBrowse to view multiple genomes and compare their differences in genes?



Thanks,

Matt Wiese

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Umair Seemab | 24 Jun 11:12 2015
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multiple scaffold download

Hi,

My name is Umair and I was trying to download scaffold sequence of  
Pogona  
(https://genomics.canberra.edu.au/gbrowse/gbrowse/pogona_pvi1.1/). It  
is possible to download one scaffold sequence but I need to know is  
there any way to download multiple scaffolds at once. I shall wait for  
your reply. Thanks.

Best,
Umair

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Elisabetta Manduchi | 18 Jun 22:56 2015

BAM coverage, paired-end data, overlapping mates: is there double-counting?

Hello,
I have a question about the following scenario. If I generate a coverage 
wiggle_xyplot track from a bam file that comes from a paired-end 
dataset, what happens if a read pair has overlapping mates? Will the 
overlapping region from this pair contribute a count of 1 to the 
coverage (which would be the correct way of doing this) or will there be 
any double-counting?
Thanks,
Elisabetta

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v singh | 5 Jun 21:23 2015
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OSX Yosemite install, tests fail

Hi,

I have been trying to (unsuccessfully) install GBrowse on MacOSX Yosemite. I have managed to reduce the number of failing tests from 7/10 to 3/10 now. I installed GBrowse anyways despite the failing tests, so now the index page and tutorials load but the 'yeast' example etc. do not load (Not found on server). 

Below is given the output of Build tests, I have seen another thread about CGI warnings but the errors in mine are different. I will be grateful for any pointers on how to fix these errors and get my GBrowse up and running.

Also, when I tried to build the demo, I got the following error --

-------------------
$ ./Build demo
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
Creating include file for Apache config: blib/etc/apache2/other/gbrowse2.conf
httpd: Syntax error on line 22 of /var/folders/3x/9zfph_ls2m5g22jz14vjzsrwgn7xtt/T/GBrowse_demo_PNlL/conf/httpd.conf: Cannot load /opt/local/apache2/modules/mod_log_config.so into server: dlopen(/opt/local/apache2/modules/mod_log_config.so, 10): image not found
Apache failed to start. Perhaps the demo is already running?
--------------------------

The error here (in demo) is that '/opt/local/apache2/modules/mod_log_config.so' is not found, but in OSX10.10 Yosemite .. the modules for apache are stored in /usr/libexec/apache2/ instead. How can I fix this problem?

Thanks!

----------------------------------------------------
$ ./Build test

NOTE: Run ./Build reconfig to change existing configuration.
/etc/apache2/other/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.
t/00.compile.t ............ ok     
t/01.yeast.t .............. ok   
t/02.rearchitecture.t ..... ok     
t/03.render.t ............. 1/150 CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 285, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 306, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 285, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 177, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 177, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 177, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm line 177, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
t/03.render.t ............. 104/150 http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57078; search failed: 500 Can't connect to localhost:57078 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57077; search failed: 500 Can't connect to localhost:57077 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
t/03.render.t ............. ok       
t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
t/04.remoteserver.t ....... 1/43 CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57130; search failed: 500 Can't connect to localhost:57130 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57129; search failed: 500 Can't connect to localhost:57129 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
t/04.remoteserver.t ....... 3/43 Storable binary image v33.97 more recent than I am (v2.9) at /System/Library/Perl/5.18/darwin-thread-multi-2level/Storable.pm line 417, at t/04.remoteserver.t line 131.
t/04.remoteserver.t ....... Dubious, test returned 61 (wstat 15616, 0x3d00)
Failed 40/43 subtests 
(less 1 skipped subtest: 2 okay)
t/05.deferredrendering.t .. 1/19 CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2359, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2368, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2378, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2395, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2403, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2442, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
CGI::param called in list context from /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 2446, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /Library/Perl/5.18/CGI.pm line 404.
http://localhost:57139; search failed: 500 Can't connect to localhost:57139 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
http://localhost:57140; search failed: 500 Can't connect to localhost:57140 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564.
t/05.deferredrendering.t .. 4/19 [1682] rendering error track:  Can't connect to localhost:57140 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 3695.
[1682] rendering error track:  Can't connect to localhost:57140 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm line 3695.
t/05.deferredrendering.t .. Failed 5/19 subtests 
t/06.featuresearch.t ...... 1/26 http://localhost:57157; search failed: 500 Can't connect to localhost:57157 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
http://localhost:57156; search failed: 500 Can't connect to localhost:57156 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
http://localhost:57157; search failed: 500 Can't connect to localhost:57157 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
http://localhost:57156; search failed: 500 Can't connect to localhost:57156 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
http://localhost:57157; search failed: 500 Can't connect to localhost:57157 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
http://localhost:57156; search failed: 500 Can't connect to localhost:57156 (Connection refused) at /Users/vasantis/Software/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 564, <> line 45.
t/06.featuresearch.t ...... Failed 3/26 subtests 
t/07.balancer.t ........... ok     
t/07.karyotype.t .......... ok   
t/08.calign.t ............. ok   

Test Summary Report
-------------------
t/04.remoteserver.t     (Wstat: 15616 Tests: 4 Failed: 1)
  Failed test:  3
  Non-zero exit status: 61
  Parse errors: Bad plan.  You planned 43 tests but ran 4.
t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 5)
  Failed tests:  7, 11, 14, 18-19
t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)
  Failed tests:  24-26
Files=10, Tests=424, 24 wallclock secs ( 0.07 usr  0.03 sys +  9.78 cusr  3.01 csys = 12.89 CPU)
Result: FAIL
Failed 3/10 test programs. 9/424 subtests failed.

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张丹 | 4 Jun 09:37 2015
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GBrowser Tutorial

Hi Sir,
    I want to use GBrowse in my ubantu. It seems I have installed apache succefully.



Then I tried to show the volvex in the browse. All the other links can be opened except http://localhost/cgi-bin/gb2/gbrowse/volvox.
The result is as followings. Can you give me some solutions?




--
----------------------------------------------------------------------------

Dan Zhang

Computational & Evolutionary Genomics Group
Institute of Zoology, CAS
Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
Tel: +86-10-64806338



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Thomas LETELLIER | 3 Jun 14:22 2015
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Best way to link short sequences to feature

Hi,

I am working on a GBrowse (v 2.33) and I would like to display short 
sequences (between 30 and 50 nucleotides) which are linked to my 
features (BAC in my case). I can have one or several sequences per BAC.

I work on a BioDBGFF database schema and I use GFF3 files as input.

My first idea was to put these sequences into the 9 column of the GFF3 
and then display them in the "Details report" section. Because of their 
length (<50) I think that the display will be clear.

Do you think that there is a best way to handle the display of these 
sequences ?

Best regards,

Thomas

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张丹 | 2 Jun 10:16 2015
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call for binary distribution of GBrowse,sir

Dear Sir,

        Your GBrowse is so fantastic.  But I encountered some problem when I was installing it. Apache and ActiveState Perl have been be installed in my computer under windows system. Then I went to install GBrowse in your mannual.

When I tried it,  it gave me the following info .
Then I wonder whether you gave me the right URL or can you tell me other solutions to use this software. I really need your GBrowse.
Thanks so much!

----------------------------------------------------------------------------

Dan Zhang

Computational & E volutionary Genomics Group
Institute of Zoology, CAS
Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
Tel: +86-10-64806338



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John Portwood | 28 May 17:53 2015
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Scaling issues when using the wiggle_xyplot glyph on BigWigSet track

Hello,

I have a BigWigSet track which consists of four subtracks. The track looks nice for the most part, but when the subtracks are overlapped in the semi-transparent view the scaling makes the plots look misleading.

For example, in the screenshot below you can see the max values for each scale are: 287, 992, and 373, 456. The different scales make all the plots look similar which is fine for this view, but it would be ideal if they could be autoscaled based on the highest value among all subtracks for the displayed region (i.e, for this region it would be ideal if all the scales had a max value of 992). Is such a task possible without setting an arbitrary "max_score"?  


Now, the "Semi-transparent overlap" view would suit my preferences quite nicely if the overlap plots adopted the scale with the highest max value. However, this view chooses to use the 2nd highest scale (456 in this sample region). Thus, the resulting view looks misleading:

 

Using the "autoscale = chromosome" option fixes the scales for the most part, but in this dataset the values can reach as high as 8,000 which makes the plots look tiny for regions like this. So ideally I'd like to have the max value calculated into the scale based only on the region currently displayed. I'm not too familiar with BigWigs, but it seems one option would be to use a subroutine in the "max_score" conf variable, and have it return the highest max value among all the subtracks for a given region. Is such a thing possible for the Bio::DB::BigWigSet features?

Any advice would be greatly appreciative.

Thanks!
--
John Portwood
1028 Crop Genome Informatics Laboratory 
Iowa State University - USDA - ARS
Ames, IA 50010
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Ashwini M | 22 May 07:40 2015
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Problem with running Volvox

Hi,

I have installed gbrowse successfully. Following the tutorial I started with volvox database. After all the steps when I go to https://localhost/cgi-bin/gb2/gbrowse/volvox/ it says

Can't call method "get_feature_by_name" on an undefined value.

Could you please let me know why this could be happening.

I will be happy to provide any other information.

Regards,
Ashwini M

--
Ashwini M Next-Generation Genomics Laboratory Centre for Cellular and Molecular Platform National Centre for Biological Sciences Bangalore BioCluster, NCBS-GKVK Campus Bangalore 560065, India Lab Phone:    91-080-67185105 www.ccamp.res.in/NGS-Genomics
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Andy Pham | 22 May 00:55 2015
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New Dataset for GBrowse not working

Hi,
I just finished loading loading a dataset into a postgres sql database using:
bp_seqfeature_load -c -d 'dbname=gb_maes_publicgenomev4_g_gff3;host=****' -a 'DBI::Pg' -u **** -p **** Maes.gff3

However, when I try to open the URL to see the gbrowse for this particular dataset, it redirects to another dataset. I've tried restarting the apache service and triple checking the names of both the database and the config files to see if they match up.

The GBrowse.config has this in it:

[maes_genomev4]
description  = M.esculenta (Cassava) Genome v4.1
path         = maes.conf

The maes.conf file is attached. Previous datasets have successfully loaded before but for some reason this dataset is giving us problems. I have also checked the sql database and there is data in that database, so the gff3 file loaded successfully. The permissions for the files have been checked as well. The server just doesn't seem to see the changes in the config files. 

Attachment (maes.conf): application/octet-stream, 4810 bytes
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