Install DOCK 6

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NOTE FOR WINDOWS USERS: DOCK and its accessories must be run using a Linux-like environment like Cygwin ( http://www.cygwin.com/ ). When you install your emulator, make sure to also install compilers, unix shells, and perl ( Devel for Cygwin ). All steps below should be performed using Cygwin or another Windows-based Linux emulator.

(1) Decompress and extract folders using the following commands:

[user@dock ~] tar -zxvf dock.6.0.tar.gz

(2) Enter the installation directory

[user@dock ~] cd dock6/install

(3) Configure the Makefile for the appropriate operating system

[user@dock ~] ./configure [configuration file]

AUTHOR: Scott Brozell

USAGE: configure [-help] [configuration file]

OPTIONS

       -help #emit the usage statement
       configuration file #input file containing operating system appropriate variables
       Configuration Files 	Target
       gnu 	gnu-style compiler
       gnu.parallel 	gnu-style compiler with parallel processing library capability
       gnu.pbsa 	gnu-style compiler with PB/SA (ZAP library) capability
       gnu.parallel.pbsa 	gnu-style compiler with parallel processing library and PB/SA (ZAP library) capabilities
       sgi 	sgi-style compiler
       sgi.parallel 	sgi-style compiler with parallel processing library capability
       DESCRIPTION:
       Create the DOCK configuration file, config.h, by copying an existing configuration file that is selected using the arguments. When invoked without arguments, print this usage statement and if the configuration file exists then print its creation stamp. Some configuration files require that environment variables be defined; these requirements are listed in the files and emitted by configure.
   (4) OPTIONAL: Define environment variables.

(i) DOCK with parallel processing functionality requires a Message Passing Interface (MPI) library. Because of the vagaries of MPI libraries, building parallel DOCK has more pitfalls than installing the serial version. The MPI library must be installed and running on the system if the parallel features of DOCK are to be used.

       Currently, the DOCK installation mechanism only directly supports the MPICH2 and MPICH implementations. The MPICH2 library is freely available from Argonne National Labs ( http://www-unix.mcs.anl.gov/mpi/mpich/ ). Once MPI is installed, define the environment variable MPICH_HOME to the top level MPICH2 directory.
       WARNING: The parallel configuration files have been tailored to a typical MPICH2 build. Linking problems, such as undefined references and cannot find libbla_bla, can occur due to idiosyncrasies in the MPI installation. One corrective approach is to use manual linking; add to the LIBS definition in config.h the link flags (-L and -l) from the command: $MPICH_HOME/mpicc -show; in general, the LIBS should contain those link flags in the same order.
       (ii) DOCK with PB/SA scoring requires the OpenEye ZAP library. The ZAP library can be obtained from OpenEye (http://www.eyesopen.com/). Once ZAP is installed, define the environment variable ZAP_HOME to the directory that contains the ZAP library.
   (5) Build the desired DOCK executable(s)
       [user@dock ~] make all # builds all the DOCK programs
       [user@dock ~] make dock # builds only the dock program
       [user@dock ~] make utils # builds only the accessory programs
   (6) Test the built executable(s)
       [user@dock ~] cd test
       [user@dock ~] make clean
       [user@dock ~] make test
       This directory contains the DOCK quality control (QC) suite. It produces pass/fail results via fast regression tests. The suite should complete in less than ten minutes; un-passed tests should be examined to determine their significance.
       If failures occur, examine problems using the command
       [user@dock ~] make check
       NOTE: Due to differences in the random number generator and precision keeping in various operating systems, you may find differences in the exact numbers resulting in failure. We are working on increasing DOCK's resilience to these issues. For now, please ignore these failures.
       If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.