[Gmod-ajax] JBrowse SamTools setup.sh Fail

[Volodymyr Zavidovych]

Dear GMOD support team

I'm trying to install JBrowse for our small lab. We are running EC2 Amazon Linux instance. I've installed all the prerequisites. I then ran setup.sh script and everything went smoothly except that SamTools failed to install. I'm having a hard time identifying the reason of the failure. I'd really appreciate if you could help. The setup.log file is attached.

Thank you

Vovan

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[Robert Buels-2]

You're also running into the -fPIC samtools compilation issue
(http://generic-model-organism-system-database.450254.n5.nabble.com/Bio-DB-Sam-installation-problem-td4397268.html 
if you really want to know the details).

Just run this command in your jbrowse directory and run setup.sh again:

perl -i -pE 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/'
samtools/Makefile;


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 06/05/2012 05:07 AM, Volodymyr Zavidovych wrote:

> Dear GMOD support team
>
> I'm trying to install JBrowse for our small lab. We are running EC2
> Amazon Linux instance. I've installed all the prerequisites
> <http://gmod.org/wiki/JBrowse_Troubleshooting>. I then ran setup.sh
> script and everything went smoothly except that SamTools failed to
> install. I'm having a hard time identifying the reason of the failure.
> I'd really appreciate if you could help. The setup.log file is attached.
>
> Thank you
> Vovan
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-ajax mailing list
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[Robert Buels-2]

You're also running into the -fPIC samtools compilation issue
(http://generic-model-organism-system-database.450254.n5.nabble.com/Bio-DB-Sam-installation-problem-td4397268.html 
if you really want to know the details).

Just run these commands in your jbrowse directory and run setup.sh again:

make -C samtools clean;
perl -i -pE 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/'
samtools/Makefile;


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 06/05/2012 05:07 AM, Volodymyr Zavidovych wrote:

> Dear GMOD support team
>
> I'm trying to install JBrowse for our small lab. We are running EC2
> Amazon Linux instance. I've installed all the prerequisites
> <http://gmod.org/wiki/JBrowse_Troubleshooting>. I then ran setup.sh
> script and everything went smoothly except that SamTools failed to
> install. I'm having a hard time identifying the reason of the failure.
> I'd really appreciate if you could help. The setup.log file is attached.
>
> Thank you
> Vovan
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[Volodymyr Zavidovych]

Worked like charm, thanks Robert!

Vovan

On Tue, Jun 5, 2012 at 5:54 PM, Robert Buels <[hidden email]> wrote:

You're also running into the -fPIC samtools compilation issue (http://generic-model-organism-system-database.450254.n5.nabble.com/Bio-DB-Sam-installation-problem-td4397268.html if you really want to know the details).

Just run these commands in your jbrowse directory and run setup.sh again:

make -C samtools clean;

perl -i -pE 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/' samtools/Makefile;


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 06/05/2012 05:07 AM, Volodymyr Zavidovych wrote:

Dear GMOD support team

I'm trying to install JBrowse for our small lab. We are running EC2
Amazon Linux instance. I've installed all the prerequisites

<http://gmod.org/wiki/JBrowse_Troubleshooting>. I then ran setup.sh

script and everything went smoothly except that SamTools failed to
install. I'm having a hard time identifying the reason of the failure.
I'd really appreciate if you could help. The setup.log file is attached.

Thank you
Vovan

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/



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--

Volodymyr (Vovan) Zavidovych

Pratt School of Engineering '14

Duke University

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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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