CCL: Step by step instructions for installing OpenEye software in Ubuntu 10.04 and 9.10




Dear CCL list members,

this weekend I have been successful running the latest OpenEye software versions with Ubuntu 10.04 and 9.10 (64 bits) and I think that the "how to do" information can be of help for some of you [I have used some information that kindly provided to me Vincent Leroux, Greg Warren and Joe Corkery to my question to the CCL list "Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?" last 29/10/2009]:

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_DIR=/home/gerard/MolBioSoft/openeye
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:

mkdir /tmp/libstdc++5
cd /tmp/libstdc++5
wget http://mirrors.kernel.org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_amd64.deb
wget http://mirrors.kernel.org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_i386.deb
sudo updatedb
locate libstdc++.so.

sudo dpkg --force-architecture -i libstdc++5_3.3.6-17ubuntu1_i386.deb
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) !!!


Hope this helps

Best

Gerard

--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
Nutrigenomics Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia