<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>
