/usr/share/doc/garlic-doc/install/index.html

<html>

<head>
<title>
Garlic Installation
</title>
</head>

<h1 align=center>

Garlic Installation

</h1>

<hr size="3">

<font size="-1" color="red">
garlic,
free molecular viewer and editor,
free molecular visualization program,
protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule,
Unix, Linux, free software download, open source software,
Damir Zucic.
</font>

<hr size="3">

<b>
<font color="red">
Package maintainers, please read
</font>
<a href="../config/important_files.html">
this text
</a>
<font color="red">
first!
</font>
</b>

<hr size="3">

Garlic is the most portable molecular viewer/editor in the Unix world,
because the only libraries required by this program are the standard C library
(libc), the standard math library (libm) and the standard X library (libX11).
All other molecular visualization programs require some additional libraries.
<br><br>

Before starting the installation, you might be interested to check the
<a href="../techinfo/index.html">
technical requirements
</a>
. Most contemporary Unix and Unix-like systems (like Linux) meet these
requirements without need to change the configuration, so you can skip this
text if you are impatient.
<br><br>

If you have Apple McIntosh running Xtools from Tenon, please read
<a href="macosx.html">
these hints
</a>
, contributed by Chris from Macinchem.
<br><br>

To compile and install garlic, follow these instructions:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="center">

(1)

</td>

<td align="left">

Put garlic package (garlic-1.6.tar.gz) into some empty directory.

</td>

<tr>

<td align="center">

(2)

</td>

<td align="left">

Uncompress and unpack the package:
<br>

<font color="red">

gzip -d garlic-1.6.tar.gz
<br>
tar xf garlic-1.6.tar

</font>

<tr>

<td align="right">

(3)

</td>

<td align="left">

Change your working directory:
<br>


<font color="red">

cd garlic-1.6

</font>

<tr>

<td align="right">

(4)

</td>

<td align="left">

Check which C compiler is available on your system.
<br>
If you don't know how to find this information, try this:
<br>


<font color="red">

man -k compiler
<br>

</font>


to obtain the list of available compilers.


<tr>

<td align="right">

(5)

</td>

<td align="left">

If gcc (GNU C) compiler is not available on your system,
<br>
use your favorite editor to edit Makefile. Replace gcc in:
<br>


<font color=MAGENTA>

CC = gcc
<br>

</font>


line with the name of your compiler (this may be cc, for example).
<br>
If gcc is available on your system, do not change the CC line.


<tr>

<td align="right">

(6)

</td>

<td align="left">

Find a directory which contains the Xlib library. Try this:
<br>


<font color="red">

cd /
<br>
find . -name libX11\*
<br>

</font>


Check where is the file libX11.so (sharable library - prefered)
<br>
or libX11.a (static library - reserve option).
<br>
If your directory is different from /usr/X11R6/lib, modify the line:
<br>


<font color=MAGENTA>

LIBPATH = -L/usr/X11R6/lib
<br>

</font>


in Makefile. For example, if libX11.so is stored in /usr/shlib
<br>
directory on your system, the LIBPATH should be changed to:
<br>
LIBPATH = -L/usr/shlib


<tr>

<td align="right">

(7)

</td>

<td align="left">

Compile the package - just type:
<br>


<font color="red">

make
<br>

</font>


and wait, it will take some time.


<tr>

<td align="right">

(8)

</td>

<td align="left">

If everything worked fine, copy the executable to a choosen directory.
<br>
/usr/local/bin may be a good choice. This job should be done by root
<br>
(system administrator):
<br>


<font color="red">

cp garlic /usr/local/bin
<br>

</font>


If you don't have root privileges, ask your local administrator to install
<br>
garlic, or just leave it in one of your directories.


<tr>

<td align="right">

(9)

</td>

<td align="left">

Now the .garlicrc configuration file and the file which contains the
<br>
template residues should be copied to a directory where these files 
<br>
will be accessible to everyone. If this is not done, garlic will work
<br>
anyway, using hard-coded default configuration, but you will be unable
<br>
to replace residues and to create peptides.
<br>
The recommended directory is /usr/share/garlic (since January 2006).
<br>
This directory and two default files should be should be prepared by
<br>
the system administrator or by the "sudoer":
<br>


<font color="red">

mkdir /usr/share/garlic
<br>
cp .garlicrc /usr/share/garlic
<br>
cp residues.pdb /usr/share/garlic
<br>

</font>

<tr>

<td align="right">

(10)

</td>

<td align="left">

It may be good idea to copy the configuration file to your home directory
<br>
or to the subdirectory garlic of your home directory. The same may be
<br>
done with the file residues.pdb. If you do this, you will be able to
<br>
personalize your garlic sessions, because your private files will override
<br>
the system-wide defaults. Of course, you don't need root privileges
<br>
to do this:
<br>


<font color="red">

cp .garlicrc $HOME
<br>
cp residues.pdb $HOME
<br>

</font>


or:
<br>


<font color="red">

mkdir $HOME/garlic
<br>
cp .garlicrc $HOME/garlic
<br>
cp residues.pdb $HOME/garlic
<br>

</font>

<tr>

<td align="center">

(11)

</td>

<td align="left">

It is recommended to set the environment variable MOL_PATH, so garlic
<br>
will search all directories listed in this variable to find the specified
<br>
file. Click
<a href="mol_path.html">
here
</a>
for detailed instructions.


<tr>

<td align="right">

(12)

</td>

<td align="left">

Clean up the mess (sources and .o files). Be sure to leave all .pdb files
<br>
for later practice. Leave also the files with the extension .script, these
<br>
are some garlic tutorial scripts.


</table>


<br>
If garlic refuses to work because it fails to get the TrueColor visual,
try to execute
<br>
<font color="red">
xdpyinfo
</font>
and
<font color="red">
xwininfo
</font>
(click into the root window); check the list of supported visuals
<br>
and the current color depth.
Choose the color depth for which the TrueColor visual
<br>
is available. If you have the SGI Octane workstation, please read
<a href="octane.html">
this text
</a>
,
<br>
contributed by Randal R. Ketchem. If you have IBM RS6000 with AIX,
read
<a href="rs6000.html">
this
</a>
<br>
hint, contributed by Nicolas Ferre.
<br><br>



The list of sites with proteins, nucleic acids and hetero compounds is
<a href="../data/index.html">
here
</a>
.
<br><br>



If you can't compile, install or run garlic, write to me (Damir Zucic),
<br>
my address is
<a href="mailto:zucic@mefos.hr">
zucic@mefos.hr
</a>
.


<hr size="3">

</html>
garlic-doc 1.6-1 / usr / share / doc / garlic-doc / install / index.html
