Installing PThread on linux for tophat - linux

Question

Bowtie 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.
I downloaded PThread from this website. 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.
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; \
then mv -f ".deps/PThreadRun.Tpo" ".deps/PThreadRun.Plo"; else rm -f ".deps/PThreadRun.Tpo"; exit 1; fi
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()':
PThreadRun.cpp:28:38: error: 'redirectPthreadRun' was not declared in this scope
make: * [PThreadRun.lo] Error 1
make: Leaving directory `/install_dir'
make: * [all-recursive] Error 1
make: Leaving directory `/install_dir'
make: * [all] Error 2
Anyone knows how to solve this?

Answer 1

You need to run configure first. Per the installation instructions:
These are generic installation instructions.
The configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create aMakefile' in each directory of the package.
It may also create one or more .h' files containing system-dependent
definitions. Finally, it creates a shell scriptconfig.status' that
you can run in the future to recreate the current configuration, and a
file config.log' containing compiler output (useful mainly for
debuggingconfigure').
It can also use an optional file (typically called config.cache'
and enabled with--cache-file=config.cache' or simply `-C') that
saves the results of its tests to speed up reconfiguring. (Caching is
disabled by default to prevent problems with accidental use of stale
cache files.)
If you need to do unusual things to compile the package, please try
to figure out how configure' could check whether to do them, and mail
diffs or instructions to the address given in theREADME' so they can
be considered for the next release. If you are using the cache, and
at some point `config.cache' contains results you don't want to keep,
you may remove or edit it.
The file configure.ac' (orconfigure.in') is used to create
configure' by a program calledautoconf'. You only need
configure.ac' if you want to change it or regenerateconfigure'
using a newer version of `autoconf'.
The simplest way to compile this package is:
cd' to the directory containing the package's source code and type
./configure' to configure the package for your system. If you're
using csh' on an old version of System V, you might need to type
sh ./configure' instead to prevent csh' from trying to execute
configure' itself.
Running `configure' takes awhile. While running, it prints some
messages telling which features it is checking for.
Type `make' to compile the package.
Optionally, type `make check' to run any self-tests that come with
the package.
Type `make install' to install the programs and any data files and
documentation.
You can remove the program binaries and object files from the
source code directory by typing make clean'. To also remove the
files thatconfigure' created (so you can compile the package for
a different kind of computer), type make distclean'. There is
also amake maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.