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POInstalling PThread on linux for tophat
 

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  1. POInstalling PThread on linux for tophat
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    <p><a href="http://bowtie-bio.sourceforge.net/index.shtml" rel="nofollow">Bowtie</a> is a program which is needed for tophat. I need this program to map a few hundredmilion reads against a reference genome. Bowtie does the mapping part, this needs many CPU. In the manual of bowtie there is an option to do this multithreaded, but the library PThread needs to be installed.</p> <p>I downloaded PThread from <a href="http://staff.science.uva.nl/~bterwijn/Projects/PThread/" rel="nofollow">this website</a>. Extracted this to my program folder, opened a shell and was standing in this directory. When entering the command 'make', I get this error and I don't know how to solve this.</p> <hr> <blockquote> <p>if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -Wall -g -O2 -MT PThreadRun.lo -MD -MP -MF ".deps/PThreadRun.Tpo" -c -o PThreadRun.lo PThreadRun.cpp; \</p> <p>then mv -f ".deps/PThreadRun.Tpo" ".deps/PThreadRun.Plo"; else rm -f ".deps/PThreadRun.Tpo"; exit 1; fi</p> <p>g++ -DHAVE_CONFIG_H -I. -I. -I. -Wall -g -O2 -MT PThreadRun.lo -MD -MP -MF .deps/PThreadRun.Tpo -c PThreadRun.cpp -fPIC -DPIC -o .libs/PThreadRun.o PThreadRun.cpp: In member function 'pthread_t PThreadRun::start()':</p> <p>PThreadRun.cpp:28:38: error: 'redirectPthreadRun' was not declared in this scope</p> <p>make: <em>*</em> [PThreadRun.lo] Error 1</p> <p>make: Leaving directory `/install_dir'</p> <p>make: <em>*</em> [all-recursive] Error 1</p> <p>make: Leaving directory `/install_dir'</p> <p>make: <em>*</em> [all] Error 2</p> </blockquote> <hr> <p>Anyone knows how to solve this?</p>
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    1. COLook into http://staff.science.uva.nl/~bterwijn/Contact/ and send a polite email to the author of the software....
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      1. POInstalling PThread on linux for tophat
      1. USBasile Starynkevitch
    2. COAccording to http://bowtie-bio.sourceforge.net/manual.shtml#building-from-source it needs the "pthreads" library, which I'm 95% sure means the pthreads library which is probably already installed on your machine, rather than the "PThread" library you link to, which seems to be some C++ wrapper around pthreads.
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      1. USjanneb
 

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