v singh | 28 Jul 23:35 2015
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Fwd: SNPs by accession track

Dear All,

I want to upload a track with 250+ subtracks for displaying SNPs in samples , called  ‘SNPs by accession’ track. I generated a gff for the same looking like this —


### gff-version 3 

### source VCF file -->Example.vcf 

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 1 0;ref=C; line=Karab_062A;Name=cicar.line.kphxhfd

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 1 0;ref=C; line=Karab_062A_x_96029_02;Name=cicar.line.eq315e0

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 1 0;ref=C; line=Karab_062A_x_96029_03;Name=cicar.line.my4unk7

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 1 0;ref=C; line=Karab_062A_x_96029_16;Name=cicar.line.5wtysew

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 1 0;ref=C; line=Karab_062A_x_96029_23;Name=cicar.line.1jsnidx

Ca1 Example.vcf SNP 32031 32031 . + . acgt=0 0 2 0;ref=C; line=S2Drd_107B;Name=cicar.line.6ley7td


Here’s what I used in the config file —


[SNPbyAcc]

database     = snplines

feature      = SNP

glyph        = triangle

point        = 1

orient       = N

height       = 5

label        = 1

bgcolor      = blue

subtrack select   = Line tag_value line ;

subtrack table   =  96029;

  Bari1_092;

  Bari1_092_x_96029_01;

  Bari1_092_x_96029_02;

  Bari1_092_x_96029_03;

  Bari1_092_x_96029_05;

  Bari1_092_x_96029_07;

  Bari1_092_x_96029_08;

  Bari1_092_x_96029_09;

 

This track loads alright without the subtrack select option. once I choose the subtrack select option… essentially no data is displayed .. please see attached pdf . It will be a great help, if you can help diagnose what I’m doing wrong here. 

Many Thanks,

Vasantika
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Sofia Robb | 14 Jul 18:11 2015

searching a second DB

Hi Everyone,

I have a gbrowse 2 set up that uses two databases. The first database is in the [General] section and the 2nd is in a separate [database] stanza. I have "search options = default +autocomplete" in my 2nd Database stanza and the autocomplete is working but if I search for one of the names that pops up in the autocomplete I get 
The search timed out; try a more specific search 

Is there something else I need to add to my 2nd db stanza so that the search function works?

Thanks,
Sofia

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Ramesh krishnan Ramasamy | 12 Jul 06:06 2015
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500 internal server error

Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh
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Aimin Li | 7 Jul 04:20 2015

80 millions SNPs, track rendering error, timeout, try viewing a smaller region

Hi, everyone,
I loaded about 80 millions SNPs into GBrowse 2.55. I can view a SNP or a small region (100bp) on gbrowse.
However, it failed when viewing about 500bp or 1kbp region. The following is what I tested and configuration.

#======================
# TEST :
WEBSITE:
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/

error,failed:
1:13,026,145..13,026,244
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/?name=NUGGC

success:
1:82,234..82,534
http://res.xaut.edu.cn/cgi-bin/gb2_dspsp/gbrowse/dspsp/?name=SSCrs01000011459

#======================
# gff3: ( about 80,000,000 rows/features)
1    dspsp_general    SNP    12867    12867    .    +    .    ID=SSCrs01000012867;Name=SSCrs01000012867;Ref=T;Alt=G;dbSNPid=.
1    dspsp_general    SNP    12894    12894    .    +    .    ID=SSCrs01000012894;Name=SSCrs01000012894;Ref=A;Alt=C;dbSNPid=.
1    dspsp_general    SNP    26956    26956    .    +    .    ID=SSCrs01000026956;Name=SSCrs01000026956;Ref=C;Alt=G;dbSNPid=.
1    dspsp_general    SNP    42241    42241    .    +    .    ID=SSCrs01000042241;Name=SSCrs01000042241;Ref=T;Alt=G;dbSNPid=.
1    dspsp_general    SNP    53053    53053    .    +    .    ID=SSCrs01000053053;Name=SSCrs01000053053;Ref=T;Alt=A;dbSNPid=.
1    dspsp_general    SNP    72646    72646    .    +    .    ID=SSCrs01000072646;Name=SSCrs01000072646;Ref=A;Alt=G;dbSNPid=.
1    dspsp_general    SNP    76467    76467    .    +    .    ID=SSCrs01000076467;Name=SSCrs01000076467;Ref=T;Alt=A;dbSNPid=rs340612171
1    dspsp_general    SNP    76469    76469    .    +    .    ID=SSCrs01000076469;Name=SSCrs01000076469;Ref=A;Alt=C;dbSNPid=rs322594773

#======================
# config:
[dspsp_outgroup]
feature       = SNP:dspsp_outgroup
glyph         = triangle
point         = 1
orient        = N
height        = 6
bgcolor       = blue
fgcolor       = blue
key           = SNPs (outgroup)
category      = SNP

[dspsp_general]
feature       = SNP:dspsp_general
glyph         = triangle
point         = 1
orient        = N
height        = 6
bgcolor       = blue
fgcolor       = blue
key           = SNPs (general)
category      = SNP

#======================
# gbrowse.config:
slave_timeout          =200  
global_timeout         =300 
search_timeout         =200  

Thanks a lot!

Best wishes,
Mr Aimin Li
School of Computer Science and Technology,
Xidian University, Xi'an, China



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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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Gmane