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Old 06-24-2013, 09:52 AM   #81
GenoMax
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It appears that boost has not been compiled correctly. Do you see bjam in /home/twotwo/software/boost153/?

The link you posted is the way to build boost. You will need to replace PREFIX with the path you want for your boost libraries which would be (--prefix=/home/twotwo/software/boost153).

Last edited by GenoMax; 06-24-2013 at 10:10 AM. Reason: Clarified a file path
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Old 06-24-2013, 09:55 AM   #82
twotwo
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Quote:
Originally Posted by GenoMax View Post
Can you provide additional details?

What OS? What version of boost are you trying to compile? What is the exact command line you are using? Even if the error appears to be the same it may help us diagnose the problem if you can post it here.
The OS is the linux. And I removed some of the option:
bjam --prefix=/home/twotwo/software/boost153/ link=static runtime-link=static stage install
Then it works. Can I install without the option of:
--toolset=gcc architecture=x86 address_model=64
Is there any difference?
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Old 06-24-2013, 10:13 AM   #83
GenoMax
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Quote:
Originally Posted by twotwo View Post
The OS is the linux. And I removed some of the option:
bjam --prefix=/home/twotwo/software/boost153/ link=static runtime-link=static stage install
Then it works. Can I install without the option of:
--toolset=gcc architecture=x86 address_model=64
Is there any difference?
Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.

Last edited by GenoMax; 06-24-2013 at 10:37 AM.
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Old 06-24-2013, 12:12 PM   #84
twotwo
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Quote:
Originally Posted by GenoMax View Post
Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.
Thanks for being so helpful! Yes, I did not update my tophat since I already have my SAM files. Should I update the tophat if I only want to run cuffdiff?
And if I used
1. ./bootstrap.sh
2. ./b2 install --prefix=/home/twotwo/software/boost153
Did boost install well? Should I still need to run bjam?

Thanks so much!
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Old 06-24-2013, 12:56 PM   #85
twotwo
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Quote:
Originally Posted by GenoMax View Post
Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.
never mind my other reply. When I changed address-model from underscore to hyphen, the three options worked!!! Thank you so much!!! I felt much better.
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