Installing Projection Toolkit for Motif Finding

If you are using a linux terminal, perform the following to install projection toolkit from source file.

1. Download the source files from the terminal by using wget command. It will download the file to the present working directory

$ wget http://www.cse.wustl.edu/~jbuhler/pgt/projection-toolkit-0.42.tar.bz2

2. Unzip the tar bz2 by typing the following in the command line

$ bzip2 projection-toolkit-0.42.tar.bz2

$ tar -xxvf projection-toolkit-0.42.tar

3. Add the following line to shared-src/{alignalgos.cc, annoio.cc, parseline.cc, seqio.cc}

#include<stdlib.h>
#include<stdio.h>
#include<string.h>
4. For 64-bit architectures, comment out the line with ARCH in Makeconfig file.

#ARCH = -march=pentium3 -fomit-frame-pointer

5. Run make specifying 64-bit architecture.
make MACHINE_TYPE=i686-m64
If installation is successful, executable files will appear in the topmost level of projection-toolkit-0.42 directory.
For more information read the README file in projection-toolkit-0.42/doc/
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