[Gmod-ajax] JBrowse install error message

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[Gmod-ajax] JBrowse install error message

tszhu@fudan.edu.cn
Dear 
when I install jbrowse following the http://gmod.org/wiki/JBrowse_Configuration_Guide, all things go right, except running ./setup.sh
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
 cd /var/www/html
 unzip JBrowse-1.12.1.zip
cd JBrowse-1.12.1
./setup.sh

. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed.  See setup.log file for error messages.

Formatting Yeast example data ... failed.  See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... failed.  See setup.log file for error messages. If you really need wig-to-json.pl (most users don't), make sure libpng development libraries and header files are installed and try running setup.sh again.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...^C

And setup.log is attached here. Are there any suggestions? Thank you very much!





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setup.log (66K) Download Attachment
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Re: JBrowse install error message

nathandunn

Looks like samtools download was timing out:

===
Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
Connecting to github.com (github.com)|192.30.253.112|:443... failed: Connection timed out.
Connecting to github.com (github.com)|192.30.253.113|:443... failed: Connection timed out.
Retrying.
===

Maybe GitHub was just being flaky.  I would say try it again.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Nov 2, 2016, at 8:17 PM, [hidden email] wrote:

Dear 
when I install jbrowse following the http://gmod.org/wiki/JBrowse_Configuration_Guide, all things go right, except running ./setup.sh
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
 cd /var/www/html
 unzip JBrowse-1.12.1.zip
cd JBrowse-1.12.1
./setup.sh

. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed.  See setup.log file for error messages.

Formatting Yeast example data ... failed.  See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... failed.  See setup.log file for error messages. If you really need wig-to-json.pl (most users don't), make sure libpng development libraries and header files are installed and try running setup.sh again.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...^C

And setup.log is attached here. Are there any suggestions? Thank you very much!




<setup.log>------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: JBrowse install error message

Keiran Raine
Hi,

If you don't actually need the legacy tools to process BAMs etc to static images I'd recommend:

mv setup.sh setup.sh.orig
grep -B 1000 -F 'To see the yeast example data, browse to http' setup.sh.orig > setup.sh
chmod u+x setup.sh
./setup.sh

This removes all the legacy code setup, resulting in a much faster and leaner install.  I know there was talk of it becoming a separate script or having a param to disable this part of the install.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 3 Nov 2016, at 15:53, Nathan Dunn <[hidden email]> wrote:


Looks like samtools download was timing out:

===
Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
Connecting to github.com (github.com)|192.30.253.112|:443... failed: Connection timed out.
Connecting to github.com (github.com)|192.30.253.113|:443... failed: Connection timed out.
Retrying.
===

Maybe GitHub was just being flaky.  I would say try it again.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Nov 2, 2016, at 8:17 PM, [hidden email] wrote:

Dear 
when I install jbrowse following the http://gmod.org/wiki/JBrowse_Configuration_Guide, all things go right, except running ./setup.sh
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
 cd /var/www/html
 unzip JBrowse-1.12.1.zip
cd JBrowse-1.12.1
./setup.sh

. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed.  See setup.log file for error messages.

Formatting Yeast example data ... failed.  See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... failed.  See setup.log file for error messages. If you really need wig-to-json.pl (most users don't), make sure libpng development libraries and header files are installed and try running setup.sh again.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...^C

And setup.log is attached here. Are there any suggestions? Thank you very much!




<setup.log>------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: JBrowse install error message

nathandunn
In reply to this post by tszhu@fudan.edu.cn
I think a script for default install and install plus legacy makes sense.   Do you want to create a pr?  

Nathan

On Nov 2, 2016, at 8:17 PM, "[hidden email]" <[hidden email]> wrote:

Dear 
when I install jbrowse following the http://gmod.org/wiki/JBrowse_Configuration_Guide, all things go right, except running ./setup.sh
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
 cd /var/www/html
 unzip JBrowse-1.12.1.zip
cd JBrowse-1.12.1
./setup.sh

. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed.  See setup.log file for error messages.

Formatting Yeast example data ... failed.  See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... failed.  See setup.log file for error messages. If you really need wig-to-json.pl (most users don't), make sure libpng development libraries and header files are installed and try running setup.sh again.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...^C

And setup.log is attached here. Are there any suggestions? Thank you very much!




<setup.log>
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: JBrowse install error message

tszhu@fudan.edu.cn
In reply to this post by Keiran Raine
Thank you very much. I'll try it. May something wrong with the operation system's auto install module.


 
Date: 2016-11-04 00:15
Subject: Re: [Gmod-ajax] JBrowse install error message
Hi,

If you don't actually need the legacy tools to process BAMs etc to static images I'd recommend:

mv setup.sh setup.sh.orig
grep -B 1000 -F 'To see the yeast example data, browse to http' setup.sh.orig > setup.sh
chmod u+x setup.sh
./setup.sh

This removes all the legacy code setup, resulting in a much faster and leaner install.  I know there was talk of it becoming a separate script or having a param to disable this part of the install.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 3 Nov 2016, at 15:53, Nathan Dunn <[hidden email]> wrote:


Looks like samtools download was timing out:

===
Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
Connecting to github.com (github.com)|192.30.253.112|:443... failed: Connection timed out.
Connecting to github.com (github.com)|192.30.253.113|:443... failed: Connection timed out.
Retrying.
===

Maybe GitHub was just being flaky.  I would say try it again.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Nov 2, 2016, at 8:17 PM, [hidden email] wrote:

Dear 
when I install jbrowse following the http://gmod.org/wiki/JBrowse_Configuration_Guide, all things go right, except running ./setup.sh
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
 cd /var/www/html
 unzip JBrowse-1.12.1.zip
cd JBrowse-1.12.1
./setup.sh

. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed.  See setup.log file for error messages.

Formatting Yeast example data ... failed.  See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... failed.  See setup.log file for error messages. If you really need wig-to-json.pl (most users don't), make sure libpng development libraries and header files are installed and try running setup.sh again.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...^C

And setup.log is attached here. Are there any suggestions? Thank you very much!




<setup.log>------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax