|(1)||Put garlic package (garlic-1.5.tar.gz) into some empty directory.|
Uncompress and unpack the package:
gzip -d garlic-1.5.tar.gz
tar xf garlic-1.5.tar
Change your working directory:
Check which C compiler is available on your system.
If you don't know how to find this information, try this:
man -k compiler
to obtain the list of available compilers.
If gcc (GNU C) compiler is not available on your system,
use your favorite editor to edit Makefile. Replace gcc in:
CC = gcc
line with the name of your compiler (this may be cc, for example).
If gcc is available on your system, do not change the CC line.
Find a directory which contains the Xlib library. Try this:
find . -name libX11\*
Check where is the file libX11.so (sharable library - prefered)
or libX11.a (static library - reserve option).
If your directory is different from /usr/X11R6/lib, modify the line:
LIBPATH = -L/usr/X11R6/lib
in Makefile. For example, if libX11.so is stored in /usr/shlib
directory on your system, the LIBPATH should be changed to:
LIBPATH = -L/usr/shlib
Compile the package - just type:
and wait, it will take some time.
If everything worked fine, copy the executable to a choosen directory.
/usr/local/bin may be a good choice. This job should be done by root
cp garlic /usr/local/bin
If you don't have root privileges, ask your local administrator to install
garlic, or just leave it in one of your directories.
Now the .garlicrc configuration file and the file which contains the
template residues should be copied to a directory where these files
will be accessible to everyone. If this is not done, garlic will work
anyway, using hard-coded default configuration, but you will be unable
to replace residues and to create peptides.
The recommended directory is /usr/share/garlic (since January 2006).
This directory and two default files should be should be prepared by
the system administrator or by the "sudoer":
cp .garlicrc /usr/share/garlic
cp residues.pdb /usr/share/garlic
It may be good idea to copy the configuration file to your home directory
or to the subdirectory garlic of your home directory. The same may be
done with the file residues.pdb. If you do this, you will be able to
personalize your garlic sessions, because your private files will override
the system-wide defaults. Of course, you don't need root privileges
to do this:
cp .garlicrc $HOME
cp residues.pdb $HOME
cp .garlicrc $HOME/garlic
cp residues.pdb $HOME/garlic
It is recommended to set the environment variable MOL_PATH, so garlic
will search all directories listed in this variable to find the specified
file. Click here for detailed instructions.
Clean up the mess (sources and .o files). Be sure to leave all .pdb files
for later practice. Leave also the files with the extension .script, these
are some garlic tutorial scripts.