tophat install problem
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7.1 years ago
biolab ★ 1.4k

Hi everyone

I installed boost (prefixed at /data/xma/local/boost/), bowtie, samtools, all without problem,  but am facing tophat problem:

checking whether Boost::Thread needs Boost::System library... configure: error: Cannot use Boost::Thread

My command is ./configure --prefix=/data/xma/local/tophat/  --with-boost=/data/xma/local/boost/  --with-bam=/data/xma/tools/samtools-0.1.19

I tried adding the option  --with-boost-libdir=/data/xma/local/boost/lib,  unfortunately it does not work.  Could anyone kindly offers me solutions?  I have been in trouble for hours. Thanks a lot!!

tophat • 4.0k views
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I finally resolved the problem. The --with-boost option is wrong, should be --with-boost=/data/xma/local/boost/include/boost/.   Hope this post helps in case anyone else meet the same problem.

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6.1 years ago
mmfansler ▴ 370

Ran in to exactly the same error, but neither of the above were the issue for me. Perhaps unique to the fact that I have boost installed through macports, my system only has libboost_system-mt in the lib directory and was not being recognized. Adding a soft link for libboost_system in the same directory was all I needed. Was smooth sailing from there on out.

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Thank you!!!! This perfectly fixed my issue.

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6.4 years ago

Hello,

I just ran into the same issue with tophat, but the above solution didn't work for me.

./configure --prefix=path/to/install --with-boost=boost/base/dir/

(boost/base/dir needs to include two directories - "include" and "lib")

For me, tophat's small example script at configure's line 5558 to test for Boost:Thread didn't work properly (in the step "checking whether Boost::Thread needs Boost::System library..."), here's the error message from the logs (you can get the logs in "config.log" with ./configure --enable-debug)

thread.cpp:(.text+0xdb): undefined reference to `clock_gettime'

In the configure script, I had to change this line

CXXFLAGS="-pthread $CXXFLAGS"

to

CXXFLAGS="-pthread -lrt $CXXFLAGS"

Using the -lrt flag adds the "Real Time" library to compilation, which adds that missing method.

I also had to add "-lrt" to src/Makefile in CXXFLAGS

Then, running make produced the correct binaries. It seems to differ between systems. I'd recommend to always use the pre-compiled binaries.

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