DEODAS is made up of a number of programs. Some programs are prerequisites commonly found in Linux systems and others are installed with DEODAS. Most DEODAS programs have been packaged in RedHat Package Management (RPM) format for easy installation. DEODAS also needs Genbank flat files for analyzing designed oligonucleotides. DEODAS stores its results with the Postgresql database management system (DBMS). The database must be initialized and users must be enabled before using DEODAS. These topics are covered in detail in the sections below.
DEODAS is available in source code and some parts are in binary RPM packages from the web site at http://deodas.sourceforge.net/.
DEODAS is made of several parts. The components come as source code in the compressed archive `DEODAS_src.tar.gz'. One component, EMBOSS, does not come with DEODAS because it is in rapid development. EMBOSS is down-loadable from
http://www.uk.embnet.org/Software/EMBOSS/. The archive decompresses into the directory `DEODAS_src/' and the subdirectories `DEODAS/', `support/' and `htdocs/'. DEODAS contains programs written specifically for DEODAS. Support contains programs by other authors collected here for convenience to users. Htdocs contains a copy of the DEODAS web site. These directories have further subdirectories for each component. The directories are arranged this way so that `DEODAS/' can be kept separately on Current Version System (CVS) and programs can be easily plugged in and out in future versions of DEODAS. The licensing of each program is covered separately in its subdirectory. The program directories are outlined below.
DEODAS was developed on Intel Pentium processors with RedHat Linux 6.2. Most DEODAS programs also come as source and binary RPMs. DEODAS should also work on other Linux and POSIX or UNIX type systems that have the required libraries and programs described below. The sources and packages are outlined:
DEODAS uses a modified version of the program mablock. The modified source file is in this distribution and is in `DEODAS_src/DEODAS/extra/'. The mablock program normally checks the file type after opening a file but this causes a SEGMENTATION FAULT when using Glibc 2.1 or newer libraries when opening clustalw alignment files. In the BLIMPS `mablock.c' file, seq_type was set to AA_SEQ.
mablock.c: line 186: seqtype = AA_SEQ;
The original `mablock.c' file is included with the extension .orig.
Directory: `DEODAS/'
| Directory | Programs/Function | RPM package |
| `cleanfasta/' | cleanfasta removes long descriptions from FASTA files | `cleanfasta-*.*.*.i386.rpm' |
| `deodas/' | deodas.py is the main interface, deodasdesigner.py designs oligos | `deodas-*.*.*.i386.rpm' |
| `deodasquery/' | deodasquery is for analysis of design results | `deodasquery-*.*.*.i386.rpm' |
| `deodas-doc/' | Installation guide, manuals and tutorials | `deodas-doc-*.*.*.i386.rpm' |
| `extra/' | SQL scripts and modified files of supporting programs for developers | none |
| `libdbg/' | C function library with debugging for splittree | `libdbg-*.*.*.i386.rpm' |
| `libodbccppwrap/' | C++ ODBC class used in deodasquery | `libodbccppwrap-*.*.*.i386.rpm' |
| `libstr/' | C function library for specific string manipulation in splittree | `libstr-*.*.*.i386.rpm' |
| `splittree/' | splittree divides FASTA sequences into subgroups based on dissimilarity | `splittree-*.*.*.i386.rpm' |
Directory: `support/'
| Directory | Programs/Function | RPM package |
| `blimps-3.3.2/' | mablock finds conserved blocks, codehop designs oligos | none |
| `clustalw-1.8/' | clustalw aligns multiple sequences | `clustalw-1.8.i386.rpm' |
| `htmlize-codehop/' | htmlize-codehop converts codehop oligo output into HTML | `htmlize-codehop-*.*.*.i386.rpm' |
DEODAS uses a number of system files that usually come with Linux systems. They should be installed before DEODAS. All should come as RPM (RedHat) or DEB (Debian) packages on most Linux systems. The graphical interfaces for DEODAS are made with the GTK and Gnome toolkits. If compiling DEODAS the development libraries are needed. If installing from binary RPMs the Gnome run-time libraries are enough; if the Gnome desktop can run these are installed. Other required programs are:
deodasquery printing
Most DEODAS programs come with GNU configure scripts to automate compiling and installation. To build and install the programs in the subdirectories `cleanfasta/', `deodasquery/', `htmlize-codehop/', `libdbg/', `libodbccppwrap/',
`libstr/', and `splittree/' run: ./configure, make, and change to root to run make install. EMBOSS compiles in the same fashion but it is necessary to leave EMBOSS where it was compiled. The EMBOSS programs use definition files in
`EMBOSS/emboss/acd/'. These commands should build and install the programs in those directories. The subdirectories contain additional installation information if there is a problem.
The `deodas/' directory contain Python and Expect scripts. These install with the command make install as root user. The installation script assumes the location of Python is `/usr/lib/python1.5'. The `Makefile' under `deodas/src' will need to be altered if Python is in a different location.
The programs in `clustallw-1.8/' compile and install with make and as root run make install
The directory `blimps-3.3.2/' must be placed in the location it is going to run from. Place the directory in a location like `/usr/local' and set the environment variable BLIMPS_DIR=/usr/local/blimps-3.3.2/. This can be done several ways. To make it permanent for all users as root open the file `/etc/bashrc' and enter the lines
BLIMPS_DIR=/usr/local/blimps-3.3.2
export BLIMPS_DIR. Start a new x-terminal to activate the changes. Change into the directory `blimps-3.3.2/blimps' and compile for Linux with the command make -f Makefile.Linux.
The `bin/' directory of blimps-3.3.2 needs to be on the executable path. as root enter the a line like `export PATH=$PATH:/usr/local/blimps-3.3.2/bin' in the file `/etc/profile'.
Test the installation by running mablock and codehop. Just cancel with Crtlc after getting some output to make sure they run.
The RPM packages install with the command rpm -i RPM name, all the packages can be put on the command line together or RPMs can be installed with the graphical package manager gnorpm. The only complication is the order. Have the prerequisites installed first (see section Prerequisites). Then install the DEODAS libraries `libdbg-*.*.*.i386.rpm', `lidodbccppwrap-*.*.*.i386.rpm',
`libstr-*.*.*.i386.rpm' first. Then install the other packages:
`splittree-*.*.*.i386.rpm', `clustalw-1.8.i386.rpm',
`cleanfasta-*.*.*.i386.rpm', `htmlize-codehop', `deodas-*.*.*.i386.rpm', and
`deodasquery-*.*.*.i386.rpm'.
The programs EMBOSS and BLIMPS have to be compiled to install (see section Compiling).
Genbank flat files are available by anonymous ftp at ftp://ncbi.nlm.nih.gov in the directory `genbank/'. An Expect script is included for automating the download and installation of Genbank flat files. It will be installed as `/usr/bin/ftp.genbank.exp'. Three parts of this file need to be modified. The parts are each labeled with #TODO. So after opening this script with a text editor search for #TODO. On line 71 enter the directory to store the Genbank flat files. The user running the script must have write access to this directory. It is more secure for a normal user to run this script than the root. On line 90 enter a user e-mail address for an anonymous ftp password. On line 101 enter the Genbank files needed for this installation.
The script can be automatically ran by cron, a program that runs programs periodically. To set this up a user should run the command crontab -e. This brings up the vi text editor. Enter a line with minute hour day of month * * ftp.genbank.exp. An example could be:
15 1 1 * * ftp.genbank.exp
This would be to download Genbank on the first of each month at 1:15 am. Please make up your own numbers or we'll all be accesses the server at the same time. Then write and quit the vi text editor with :wq.
To install Postgresql database management system (DBMS) get the latest version from http://www.postgresql.org/. They come as sources and RPMs. DEODAS 0.1 was written using Postgresql 7.02. Get the RPMs if your system can install RPM packages. Install them with rpm -i package-name-*.*.*.i386.rpm or with a graphical installer like gnorpm. After installing the packages initialize the system from the root user by running the command /etc/rc.d/init.d/postgresql start.
The Postgresql DBMS needs to start when the computer starts. The K-Desktop Environment (KDE) contains a nice program for this called ksysv. Run ksysv as root user the drag postgresql to run level 5. This creates a symbolic link from
`/etc/rc.d/init.d/postgresql' to `/etc/rc.d/rc5.d/' that automatically starts the Postgresql DBMS when the computer starts up and enters run level 5.
The Postgresql is managed by the user postgres. From root change to user postgres with the command su postgres. As this user enable system users to use the DBMS run the command createuser user-name. Then answer the questions at the prompt. Postgresql comes with an extensive manual and has more information at its home page. If the user is enabled with Postgresql, DEODAS can handle database creation and connection through the graphical interface.
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