1) Download the SuSE v9.1 x86_64
software packages from the OpenEye website. In my case, I download the next
packages:
babel-3.3-suse-9.1-x86_64.tar.gz
eon-2.0.1-suse-9.1-x86_64.tar.gz
filter-2.0.2-suse-9.1-x64.tar.gz
fred-2.2.5-suse-9.1-x64.tar.gz
ogham-1.7.0-suse-9.1-x64.tar.gz
omega-2.3.2-suse-9.1-x64.tar.gz
quacpac-1.3.1-suse-9.1-x64.tar.gz
rocs-3.0.0-suse-9.1-x64.tar.gz
szybki-1.3.4-suse-9.1-x64.tar.gz
vida-4.0.0-suse-9.1-x64.tar.gz
2)
Download the RedHat Enterprise x86_64 software package from brood
brood-2.0.0-redhat-RHEL3-x64.tar.gz
3) Uncompress, for instance,
eon-2.0.1-suse-9.1-x86_64.tar.gz in your Desktop. This will create an
openeye folder that, in my case, I have moved to my
/home/gerard/MolBioSoft folder.
4) Next, uncompress a second .tar.gz package in your Desktop (for
instance
filter-2.0.2-suse-9.1-x64.tar.gz). Again, an
openeye
folder will be created in your Desktop. Move this
openeye folder to the
parent folder of the previous
openeye folder that contains yet
EON
(in my case, the
/home/gerard/MolBioSoft folder) and when the graphical
interface ask you how to manage a second
openeye folder within
/home/gerard/MolBioSoft select the
combine option. This will merge
the contents of the
openeye folder obtained by uncompress
eon-2.0.1-suse-9.1-x86_64.tar.gz and
filter-2.0.2-suse-9.1-x64.tar.gz. Proceed with the same protocol for the
rest of packages.
5) Put your
oe_license.txt license document into the resulting
openeye folder (in my case
/home/gerard/MolBioSoft/openeye)
6) Edit your
bash.bashrc configuration file (use the
sudo -s gedit
/etc/bash.bashrc command) and add at its end the next information (please
replace
/home/gerard/MolBioSoft/ in the next line by the absolute path of
your
openeye folder):
export
OE_ARCH=suse-9.1-x64
alias align="$OE_DIR/bin/align"
alias
brood="$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/brood"
alias
checkcff="$OE_DIR/bin/checkcff"
alias chunker="$OE_DIR/bin/chunker"
alias
depict="$OE_DIR/bin/depict"
alias
eon="$OE_DIR/bin/eon"
alias
filter="$OE_DIR/bin/filter"
alias
fixpka="$OE_DIR/bin/fixpka"
alias flipper="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/flipper"
alias
fred="$OE_DIR/bin/fred"
alias
hlmerge="$OE_DIR/bin/hlmerge"
alias
makefraglib="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/makefraglib"
alias makerocsdb="$OE_DIR/bin/makerocsdb"
alias
mol2gif="$OE_DIR/bin/mol2gif"
alias
mol2img="$OE_DIR/bin/mol2img"
alias
mol2ps="$OE_DIR/bin/mol2ps"
alias
molcharge="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/molcharge"
alias molprop="$OE_DIR/bin/molprop"
alias
oeb2sdconf="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/oeb2sdconf"
#alias
oempirun="$OE_DIR/bin/oempirun"
alias
omega="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/omega2"
alias openeyebabel="$OE_DIR/bin/openeyebabel"
#alias
orted="$OE_DIR/bin/orted"
alias
picto="$OE_DIR/bin/picto"
alias
pkatyper="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/pkatyper"
alias rocs="$OE_DIR/bin/rocs"
alias
szybki="$OE_DIR/bin/szybki"
alias
tautomers="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/tautomers"
alias
vbrood="$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/vbrood"
alias vida="$OE_DIR/bin/vida"
alias
vrocs="$OE_DIR/bin/vrocs"
Save and close the
/etc/bash.bashrc document
7) In order to know if
vida runs, open a new terminal (or write the
source
/etc/bash.bashrc command in a yet opened terminal) and write
vida. In
my case, the next error message occurs:
gerard{:}URV-nutrigenomica-01:~$
vida
/home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/bin/vida:
error while loading shared libraries: libstdc++.so.5: cannot open shared object
file: No such file or directory
gerard{:}URV-nutrigenomica-01:~$
This means that the libstdc++.so.5
is not in my Ubuntu distribution (and it seems that this library has been
dropped from the latest Ubuntu distributions ...). Then, I have followed the
instructions at
http://www.digitalenigma.com/directory.php?include=home
Basically they consist on writing the next commands in the command
line:
sudo
updatedb
locate libstdc++.so.
sudo mv /usr/lib/libstdc++.so.5*
/usr/lib32/.
sudo updatedb
locate libstdc++.so.
sudo dpkg -i
libstdc++5_3.3.6-17ubuntu1_amd64.deb
sudo
updatedb
locate libstdc++.so.
8) Try again if
vida runs by writing the
vida command in a new terminal (or in the
same one where you write the the
source /etc/bash.bashrc command after
updating
/etc/bash.bashrc information). In my case, the next error
message
occurs:
gerard{:}URV-nutrigenomica-01:~$
vida
/home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/bin/vida:
error while loading shared libraries: libpng.so.3: cannot open shared object
file: No such file or directory
gerard{:}URV-nutrigenomica-01:~$
Then, you need to know which is
the current version you have of the
libpng library in your computer and
use it to make a symbolic link with the filename
libpng.so.3 at the
/usr/lib folder. Thus, in order to know which is the version you have of
the
libpng library open the
synaptic utility and search for the
libpng filename. In my case, I see that the
libpng library I have
is
libpng12-0. Push the
libpng12-0 row in
synaptic with
your right-mouse button and select
Properties in order to see where is
the library installed and which is exactly its filename. In the resulting
window, select the
Installed files tab and take a look to the filenames
it shows. In my case, its name is
libpng12.so.0.42.0 and it is installed
at the
/lib folder. Then, I have written the
sudo ln -s
/lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3 command in the terminal:
gerard{:}URV-nutrigenomica-01:~$ sudo ln -s
/lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3
and now I tried again
to run
vida by writing the
vida command in a new terminal (or in
the same one
where you write the the
source /etc/bash.bashrc command after
updating
/etc/bash.bashrc information) and, it works now (and also
picto, vrocs and vbrood) !!!