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Forum: Bioinformatics 06-24-2013, 10:13 AM
Replies: 84
Views: 23,931
Posted By GenoMax
Are you using the directions for "Getting...

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...
Forum: Bioinformatics 06-24-2013, 09:52 AM
Replies: 84
Views: 23,931
Posted By GenoMax
It appears that boost has not been compiled...

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...
Forum: Bioinformatics 06-24-2013, 07:54 AM
Replies: 84
Views: 23,931
Posted By GenoMax
Can you provide additional details? What OS?...

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...
Forum: Bioinformatics 05-15-2013, 03:45 PM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, Now my head is starting to hurt :D ...

Dave,

Now my head is starting to hurt :D

I feel that all these problems are because of additional directive in red:

--with-boost=/usr/local/boost_1_53_0 --with-boost-libdir=/usr/local/lib ...
Forum: Bioinformatics 05-14-2013, 04:19 PM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, The extra "//" are there because you...

Dave,

The extra "//" are there because you used an additional trailing "/" in your "--with-bam=/usr/local/include/bam/ and --with-eigen=/usr/local/include/Eigen/". Omit the trailing slashes on...
Forum: Bioinformatics 05-14-2013, 08:00 AM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, You were missing a "/" at the...

Dave,

You were missing a "/" at the beginning of --prefix

In any case were "include" and "lib" created under "/home/mrmary/ngs/applications/"? If you were doing the compilation again I would...
Forum: Bioinformatics 05-14-2013, 03:31 AM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, There is a typo in the bjam build...

Dave,

There is a typo in the bjam build command that is included on the cufflinks "getting started (http://cufflinks.cbcb.umd.edu/tutorial.html)" page. The address model directive needs a "-"...
Forum: Bioinformatics 05-13-2013, 04:02 PM
Replies: 84
Views: 23,931
Posted By GenoMax
"include --> boost" will have all the "*.hpp"...

"include --> boost" will have all the "*.hpp" files (I see 214 files) and "lib" will have all "libboost*" files.
Forum: Bioinformatics 05-13-2013, 03:02 PM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, Do you see the two directories...

Dave,

Do you see the two directories "include" and "lib" under "/usr/local/boost_1_53_0/ " (or /home/mrmary/ngs/applications/boost_1_53_0/) ? If you don't then that means your boost libraries did...
Forum: Bioinformatics 05-13-2013, 04:39 AM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave, "--with-boost=" should point to the...

Dave,

"--with-boost=" should point to the top level directory where the "include" and "lib" directories for boost are. In your case if "/usr/local/boost_1_53_0" is that directory then your...
Forum: Bioinformatics 05-12-2013, 04:30 PM
Replies: 84
Views: 23,931
Posted By GenoMax
Dave: Where exactly did you install boost...

Dave: Where exactly did you install boost libraries? Are they in "/usr/local" or in your home directory?

You may have already seen the instructions here:...
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