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README.slide
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########################################################
Protein Structure Analysis and Design Lab
Michigan State University
Jun 19, 2008
########################################################
SLIDE runs on various Unix systems (Linux with kernel 2.4.18 or higher,
Sun SPARC running Solaris 2.5 or higher, Intel running Solaris 5.8 or higher,
and SGI Octane running Irix64).
Before installing and compiling SLIDE, the tar file has to be placed
in the directory that will contain the root directory of the global SLIDE
installation (e.g. /usr/soft/).
To install SLIDE:
1. Set the environment variable SLIDE_DIR to the root directory of
the global SLIDE installation (e.g. /usr/soft/slide).
2. Unzip and untar the slidev2.31.tar.gz using the commands:
gunzip slide_v3.0.tar.gz
tar -xfv slide_v3.0.tar
Before you do this, please remember to backup any existing versions of slide
you might have in the directory with a different name than "slide"..
3. Check the location of your system's Perl executable using the command:
which perl
Edit the first line of the install_slide.pl file from the directory
SLIDE_DIR to point to the correct location for your system's Perl
executable. If you don't have Perl, you can download it free of charge
from www.cpan.org.
4. By default, install_slide.pl will look for a gcc compiler to compile SLIDE.
If you are using a cc compiler, change line 13 from
CC = gcc to CC = cc
in the following files:
/slide/src/template/Makefile
/slide/src/interactions/Makefile
/slide/src/slide/Makefile
NOTE:
-----
Compiling SLIDE as described above *may* result in some compilation
errors/warnings on a machine with 64-bit architecture, in which case
please compile it in 32-bit compatibility mode. SLIDE should currently
be compatible with 64-bit architecture, but if you are having problems
then do this,
follow these steps:
i) While using the gcc compiler that is native to the x86 64-bit
machine, use the "-m32" option. Do this as follows.
Change each of the following makefiles:
$SLIDE_DIR/src/template/Makefile
$SLIDE_DIR/src/interactions/Makefile
$SLIDE_DIR/src/slide/Makefile
to include the -m32 option by inserting this command before
the gcc command:
COPTS = -O2 -m32
ii) Add the library files needed for 32-bit compatibility mode.
The procedure for this is:
a) Make a tar file of the needed libraries (called libs-added below)
on a 32-bit machine using these two commands:
rpm -q --list glibc glibc-devel | grep "/lib/" > /tmp/libs-added
tar cvf 32_bit_libs.tar -T /tmp/libs-added --absolute-names
b) Copy the libraries onto the 64-bit machine by running the
following command as ROOT user in the root directory:
tar xf 32_bit_libs.tar --keep-old-files
c) Check that the library files listed in the libs-added file above
are now installed in the root directory.
iii) Now, compile SLIDE by running the installation script,
install_slide.pl
5. Run "make" in the directory SLIDE_DIR.
6. To clean the distribution, run "make clean" in the directory SLIDE_DIR.