The requested URL /cgi-bin/gb2 was not found on this server.

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The requested URL /cgi-bin/gb2 was not found on this server.

xiongjie
Hi, all
 
I newly installed the gbrowse in an Bio-linux (http://nebc.nerc.ac.uk/tools/bio-linux) server,and the bioperl should be installed in the Bio-linux (bioperl 1.6.901).
I use apt-get to intall all the prerequisites, the only thing seems to get error is installing the libgd2-noxpm-dev, the system said the libgd2-noxpm have not installed, and I installed the libgd2-noxpm using apt-get. All the prompt asked settings are "Y". 
 
Then I installed the Gbrowse using "sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2", it seems no error appears.
 
The aparche seems to work, enter the "http://localhost/"  in the explorer gave "It works!"
 
But the "http://localhost/gbrowse2" gave "The requested URL /gbrowse2 was not found on this server."
 
The "/etc/gbrowse/"  directory contain the gbrowse config files, like "GBrowse.conf".
The "/var/lib/gbrowse" contain the "databases".
No gbrowse files in "/var/www" directory.
 
How can I fix this problem?
 
Best,
 
Jie
 

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Re: The requested URL /cgi-bin/gb2 was not found on this server.

Scott Cain
Hi Jie,

My recollection is that's because of the goofy way Debian folks do some things.  I think the url you need for the GBrowse homepage is http://localhost/gbrowse/gbrowse2 or something like that.  The url for the gbrowse cgi is something like http://localhost/cgi-bin/gbrowse//gbrowse I think.

I should mention that the apt-get installed GBrowse is very old (I think it's version 2.38 or 9) and we are on 2.55.  What I usually do is use apt-get to install the prereqs for GBrowse, then install Bio::Graphics and GBrowse with cpan.

Scott



On Fri, Oct 11, 2013 at 10:51 AM, njauxiongjie <[hidden email]> wrote:
Hi, all
 
I newly installed the gbrowse in an Bio-linux (http://nebc.nerc.ac.uk/tools/bio-linux) server,and the bioperl should be installed in the Bio-linux (bioperl 1.6.901).
I use apt-get to intall all the prerequisites, the only thing seems to get error is installing the libgd2-noxpm-dev, the system said the libgd2-noxpm have not installed, and I installed the libgd2-noxpm using apt-get. All the prompt asked settings are "Y". 
 
Then I installed the Gbrowse using "sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2", it seems no error appears.
 
The aparche seems to work, enter the "http://localhost/"  in the explorer gave "It works!"
 
But the "http://localhost/gbrowse2" gave "The requested URL /gbrowse2 was not found on this server."
 
The "/etc/gbrowse/"  directory contain the gbrowse config files, like "GBrowse.conf".
The "/var/lib/gbrowse" contain the "databases".
No gbrowse files in "/var/www" directory.
 
How can I fix this problem?
 
Best,
 
Jie
 

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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: The requested URL /cgi-bin/gb2 was not found on this server.

xiongjie
Hi, Scott
 
The problem have solved after do the bellow steps:
sudo apt-get remove libgd-gd2-perl
sudo apt-get install libgd2-noxpm-dev
sudo perl -MCPAN -e 'install GD'
 
and then install the Bio::Graphics and Gbrowse using CPAN. And I can access through http://localhost/gbrowse2/.
The yeast example works well, but when I configure my own database, I realized that I should install the Bio::DB::Sam Adaptor, because I used a bam file for coverage plot.
But when I install the Bio::DB::Sam Adaptor, I get bello errors:
 
[hidden email]] sudo perl ./Build.PL                                                                            [ 3:13PM]
This module requires samtools 0.1.10 or higher (samtools.sourceforge.net).
Please enter the location of the bam.h and compiled libbam.a files: /home/miaowei/software/samtools-0.1.19/
 
Found /home/miaowei/software/samtools-0.1.19//bam.h and /home/miaowei/software/samtools-0.1.19//libbam.a.
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-SamTools' version '1.39'
[hidden email]] sudo ./Build                                                                                    [ 3:14PM]
Building Bio-SamTools
make: Nothing to be done for `all'.
[hidden email]] sudo ./Build test                                                                               [ 3:14PM]
make: Nothing to be done for `all'.
t/01sam.t .. Can't load '/home/miaowei/software/Bio-SamTools-1.39/t/../blib/arch/auto/Bio/DB/Sam/Sam.so' for module Bio::DB::Sam: /home/miaowei/software/Bio-SamTools-1.39/t/../blib/arch/auto/Bio/DB/Sam/Sam.so: undefined symbol: R_alloc at /usr/lib/perl/5.14/DynaLoader.pm line 184.
 at t/01sam.t line 26.
Compilation failed in require at t/01sam.t line 26.
BEGIN failed--compilation aborted at t/01sam.t line 26.
t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/112 subtests
 
Test Summary Report
-------------------
t/01sam.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 112 tests but ran 0.
Files=1, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.41 cusr  0.05 csys =  0.51 CPU)
Result: FAIL
Failed 1/1 test programs. 0/0 subtests failed.
[hidden email]]
 
 
How can I fix it.
 
Jie
 

发件人:Scott Cain <[hidden email]>
发送时间:2013-10-11 22:57
主题:Re: [Gmod-gbrowse] The requested URL /cgi-bin/gb2 was not found on this server.
收件人:"njauxiongjie"<[hidden email]>
抄送:"gmod-gbrowse"<[hidden email]>
 
Hi Jie,

My recollection is that's because of the goofy way Debian folks do some things.  I think the url you need for the GBrowse homepage is http://localhost/gbrowse/gbrowse2 or something like that.  The url for the gbrowse cgi is something like http://localhost/cgi-bin/gbrowse//gbrowse I think.

I should mention that the apt-get installed GBrowse is very old (I think it's version 2.38 or 9) and we are on 2.55.  What I usually do is use apt-get to install the prereqs for GBrowse, then install Bio::Graphics and GBrowse with cpan.

Scott



On Fri, Oct 11, 2013 at 10:51 AM, njauxiongjie <[hidden email]> wrote:
Hi, all
 
I newly installed the gbrowse in an Bio-linux (http://nebc.nerc.ac.uk/tools/bio-linux) server,and the bioperl should be installed in the Bio-linux (bioperl 1.6.901).
I use apt-get to intall all the prerequisites, the only thing seems to get error is installing the libgd2-noxpm-dev, the system said the libgd2-noxpm have not installed, and I installed the libgd2-noxpm using apt-get. All the prompt asked settings are "Y". 
 
Then I installed the Gbrowse using "sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2", it seems no error appears.
 
The aparche seems to work, enter the "http://localhost/"  in the explorer gave "It works!"
 
But the "http://localhost/gbrowse2" gave "The requested URL /gbrowse2 was not found on this server."
 
The "/etc/gbrowse/"  directory contain the gbrowse config files, like "GBrowse.conf".
The "/var/lib/gbrowse" contain the "databases".
No gbrowse files in "/var/www" directory.
 
How can I fix this problem?
 
Best,
 
Jie
 

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the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
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Re: The requested URL /cgi-bin/gb2 was not found on this server.

Scott Cain
Hi Jie,

Sorry this slipped by for a few days.  Here is what I would do: use apt-get to install libgd, gd, bioperl and biographics, and the samtools libraries (samtools is called libbio-samtools-perl) and then update Bio::Graphics via cpan (since GD will already be installed via apt-get, updating Bio::Graphics should go fine).  

Scott



On Sat, Oct 12, 2013 at 3:24 AM, njauxiongjie <[hidden email]> wrote:
Hi, Scott
 
The problem have solved after do the bellow steps:
sudo apt-get remove libgd-gd2-perl
sudo apt-get install libgd2-noxpm-dev
sudo perl -MCPAN -e 'install GD'
 
and then install the Bio::Graphics and Gbrowse using CPAN. And I can access through http://localhost/gbrowse2/.
The yeast example works well, but when I configure my own database, I realized that I should install the Bio::DB::Sam Adaptor, because I used a bam file for coverage plot.
But when I install the Bio::DB::Sam Adaptor, I get bello errors:
 
[hidden email]] sudo perl ./Build.PL                                                                            [ 3:13PM]
This module requires samtools 0.1.10 or higher (samtools.sourceforge.net).
Please enter the location of the bam.h and compiled libbam.a files: /home/miaowei/software/samtools-0.1.19/
 
Found /home/miaowei/software/samtools-0.1.19//bam.h and /home/miaowei/software/samtools-0.1.19//libbam.a.
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-SamTools' version '1.39'
[hidden email]] sudo ./Build                                                                                    [ 3:14PM]
Building Bio-SamTools
make: Nothing to be done for `all'.
[hidden email]] sudo ./Build test                                                                               [ 3:14PM]
make: Nothing to be done for `all'.
t/01sam.t .. Can't load '/home/miaowei/software/Bio-SamTools-1.39/t/../blib/arch/auto/Bio/DB/Sam/Sam.so' for module Bio::DB::Sam: /home/miaowei/software/Bio-SamTools-1.39/t/../blib/arch/auto/Bio/DB/Sam/Sam.so: undefined symbol: R_alloc at /usr/lib/perl/5.14/DynaLoader.pm line 184.
 at t/01sam.t line 26.
Compilation failed in require at t/01sam.t line 26.
BEGIN failed--compilation aborted at t/01sam.t line 26.
t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/112 subtests
 
Test Summary Report
-------------------
t/01sam.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 112 tests but ran 0.
Files=1, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.41 cusr  0.05 csys =  0.51 CPU)
Result: FAIL
Failed 1/1 test programs. 0/0 subtests failed.
[hidden email]]
 
 
How can I fix it.
 
Jie
 

发件人:Scott Cain <[hidden email]>
发送时间:<a href="tel:2013-10-11%C2%A022" value="+12013101122" target="_blank">2013-10-11 22:57
主题:Re: [Gmod-gbrowse] The requested URL /cgi-bin/gb2 was not found on this server.
收件人:"njauxiongjie"<[hidden email]>
抄送:"gmod-gbrowse"<[hidden email]>
 
Hi Jie,

My recollection is that's because of the goofy way Debian folks do some things.  I think the url you need for the GBrowse homepage is http://localhost/gbrowse/gbrowse2 or something like that.  The url for the gbrowse cgi is something like http://localhost/cgi-bin/gbrowse//gbrowse I think.

I should mention that the apt-get installed GBrowse is very old (I think it's version 2.38 or 9) and we are on 2.55.  What I usually do is use apt-get to install the prereqs for GBrowse, then install Bio::Graphics and GBrowse with cpan.

Scott



On Fri, Oct 11, 2013 at 10:51 AM, njauxiongjie <[hidden email]> wrote:
Hi, all
 
I newly installed the gbrowse in an Bio-linux (http://nebc.nerc.ac.uk/tools/bio-linux) server,and the bioperl should be installed in the Bio-linux (bioperl 1.6.901).
I use apt-get to intall all the prerequisites, the only thing seems to get error is installing the libgd2-noxpm-dev, the system said the libgd2-noxpm have not installed, and I installed the libgd2-noxpm using apt-get. All the prompt asked settings are "Y". 
 
Then I installed the Gbrowse using "sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2", it seems no error appears.
 
The aparche seems to work, enter the "http://localhost/"  in the explorer gave "It works!"
 
But the "http://localhost/gbrowse2" gave "The requested URL /gbrowse2 was not found on this server."
 
The "/etc/gbrowse/"  directory contain the gbrowse config files, like "GBrowse.conf".
The "/var/lib/gbrowse" contain the "databases".
No gbrowse files in "/var/www" directory.
 
How can I fix this problem?
 
Best,
 
Jie
 

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
_______________________________________________
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

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
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