Instructions to install and configure EMBOSS 6.3.1

The following librairies are necessary to compile EMBOSS as well as the EMBASSY applications:

• libx11-dev
• libgd2-xpm-dev
• libpng3-dev
• libpng12-dev
• libgd-tools
• libplplot-dev
• plplot9-driver-gd
• libxaw7-dev (required for PHYLIP compilation)

% apt-get install libx11-dev libgd2-xpm-dev libpng3-dev libpng12-dev libgd-tools libplplot-dev plplot9-driver-gd libxaw7-dev

In addition, install-jemboss-server.sh installation script requires the following applications:

• Apache Tomcat (version 6.0.29 will do the trick a-ok: site Web)
• Apache AXIS 1.4 (site Web)

These applications can be deleted right after EMBOSS installation. Finally, since EMBOSS has some wrapper applications for clustalw and primer3, these applications need to be installed first.

Here is the procedure for installing EMBOSS, EMBASSY applications and the Jemboss GUI from source code:

• The archive with the EMBOSS source code is downloaded from its web location and decompressed in /home/bioubuntu. Once you are in /home/bioubuntu/EMBOSS-6.3.1, you need to create a folder called embassy. In this folder, you will download and decompressed all the EMBASSY applications and remove the archive afterward; the EMBASSY applications are found here. You need to do this since the EMBOSS install script will only compile the applications, not download them for you nor de-arcchived them. Impilo has the following EMBASSY applications:
  • CBSTOOLS-1.0.0
  • DOMAINATRIX-0.1.0
  • DOMALIGN-0.1.0
  • DOMSEARCH-0.1.0
  • ESIM4-1.0.0
  • HMMER-2.3.2
  • IPRSCAN-4.3.1
  • MEMENEW-4.0.0
  • MSE-3.0.0
  • PHYLIPNEW-3.69
  • SIGNATURE-0.1.0
  • STRUCTURE-0.1.0
  • TOPO-1.0.0
  • VIENNA-1.7.2

% wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.3.1.tar.gz
% tar -zxvf EMBOSS-6.3.1.tar.gz
% mkdir embassy
% cd embassy
#
# Do this for all EMBASSY applications
#
% wget ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.tar.gz
% tar -zxvf CBSTOOLS-1.0.0.tar.gz
#
# After all this is done...
#
% cd ..
% mv embassy EMBOSS-6.3.1

• Prepare Tomcat and AXIS:

#
# Download the archives from suggested mirrors
# For example:
#
% wget http://www.quickprepaidcard.com/apache/tomcat/tomcat-6/v6.0.29/bin/apache-tomcat-6.0.29.tar.gz
% wget http://apache.mirror.iweb.ca/ws/axis/1_4/axis-bin-1_4.tar.gz
% tar -zxvf apache-tomcat-6.0.29.tar.gz
% sudo mv apache-tomcat-6.0.29 /usr/local/share
% sudo chown -R root:root /usr/local/share/apache-tomcat-6.0.29
% tar -zxvf axis-bin-1_4.tar.gz 
% sudo mv axis-1_4 /usr/local/share
% sudo chown -R root:root /usr/local/share/axis-1_4

• Once this is done, you move the /home/bioubuntu/EMBOSS-6.3.1 folder to /opt/bio/sources/. This /opt/bio/sources/EMBOSS-6.3.1 folder should belong to root and its permissions should be set to 755.

% sudo chown -R root:root /opt/bio/sources/EMBOSS-6.1.0

• The compilation is done via an installation script called install-jemboss-server.sh found under jemboss/utils. It will ask you if Tomcat and AXIS are downloaded and functional; you say Y.

% cd /opt/bio/sources/EMBOSS-6.1.0/jemboss/utils
% sudo ./install-jemboss-server.sh

• Before actual compilation, the script will ask you several questions. In the majority of cases, the default values are OK EXCEPT for the following:

Enter java (1.4 or above) location [/usr]:
/usr/lib/jvm/java-6-sun

Type of unix password method being used 
(select 1, 2, 3, 4, 5, 6 or 7 )[3]
1

Enter Tomcat root directory (e.g. /usr/local/tomcat)
/usr/local/share/apache-tomcat-6.0.28

Enter Apache AXIS (SOAP) root directory (e.g. /usr/local/axis)
/usr/local/share/axis-1_4

• Compilation will take some time; take the time to grab a nice cup of coffee . At some point in the process, the script will ask you if you want to install the EMBASSY applications. You say Yes ans since you have downloaded everything at the right location, the default selections are a-ok.

• After some more time, the script will ask you if you want to install the EMBOSS wrapper for clustalw, and if you say yes, what is the PATH to the executable. You have to specify /usr/local/bin (voir ici) and this location is also automatically selected for the next step which is installing the EMBOSS wrapper for primer3_core.

• The script will then ask you for a password to generate the secure SSL keys for remote connections, even if you are planning a simple standalone install. Think about one and keep it safe somewhere…

• The script is continuing its work… It will ask you to modify the /usr/local/share/apache-tomcat-6.0.28/conf/server.xml file. The easiest way to do so is to open a second terminal to edit the file:

% sudo nano /usr/local/share/apache-tomcat-6.0.28/conf/server.xml

• Copy and paste the lines that shows on the first terminal instead of the lines for port 8443:

   <!-- Define an SSL HTTP/1.1 Connector on port 8443 -->
   <Connector className="org.apache.catalina.connector.http.HttpConnector"
           port="8443" minProcessors="5" maxProcessors="75"
           enableLookups="true"
           acceptCount="10" debug="0" scheme="https" secure="true">
   <Factory className="org.apache.catalina.net.SSLServerSocketFactory"
           keystoreFile="/usr/local/emboss/share/EMBOSS/jemboss/resources/server.keystore" keystorePass="bioubuntu"
           clientAuth="false" protocol="TLS"/>
   </Connector>

• It is possible that the script might not start the web container correctly; it is not important since we are not planning to do it anyway…

• Since the script install the executables in /usr/local/emboss/bin, you need to add this to the PATH. There are many ways of doing so but I chose to modify the /etc/profile file.

% sudo nano /etc/profile

• At the very end of the file, you need to add the following lines:

#
# EMBOSS specific environment variable
#
PATH=/usr/local/emboss/bin:$PATH
PAGER=/usr/bin/less

• The line PAGER=/usr/bin/less is added to facilitate navigation into the STDOUT output of the tfm command, which provides detailed instructions on all applications found in the EMBOSS suite.

• To make Jemboss functional, you need to modify the startup script /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh to make sute that is will be working in STANDALONE mode (it seems that the install-jemboss-server.sh is not so good at doing so…):

#
#Add local to run as 'standalone':
#java org.emboss.jemboss.Jemboss local &
#
/usr/lib/jvm/java-6-sun/bin/java org.emboss.jemboss.Jemboss &

become

#
#Add local to run as 'standalone':
#java org.emboss.jemboss.Jemboss local &
#
/usr/lib/jvm/java-6-sun/bin/java org.emboss.jemboss.Jemboss local &

• The EMBOSS/EMBASSY applications are now available via the command line. For Jemboss, you need to add it to the Impilo > General Purpose Applications menu:
  • More to come…

• To start Jemboss from the command line:

% sudo ln -s /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh /usr/local/bin/runJemboss
% runJemboss &

Some databases are needed to insure proper operation of some of EMBOSS' applications. Because some other programs might need them at a later moment, I created the /opt/bio/data location to centralize management of these databases. Take note of the following:

• The Codon Usage Tabulated from GenBank (CUTG) database is not part of an Impilo basic install because of its size: over 2Gb! You will have to download it yourself and follow the similar installation process as the other databases using cutgextract.

• As for TRANSFAC, since no public version exists (I will not condone bootleg versions available at some place or another on the Net), there is no Impilo install. If your lab has deep enough pockets, you can get it from here and use tfextract.

• AAINDEX : Amino acid index database
  • Web site: AAINDEX
  • Data location: ftp://ftp.genome.jp/pub/db/community/aaindex/
  • File(s) to download: aaindex1 / aaindex2 / aaindex3
  • Impilo location: /opt/bio/data/aaindex
  • EMBOSS indexer: aaindexextract

• JASPAR : Transcription factor binding site database
  • Web site: JASPAR
  • Data location: http://jaspar.genereg.net/html/DOWNLOAD/
  • File(s) to download: Archive.zip. After moving to /opt/bio/data/jaspar and unzipping, the files are under Archive/all_data/FlatFileDir.
  • Impilo location: /opt/bio/data/jaspar
  • EMBOSS indexer: jaspextract

• PROSITE : Protein signature database
  • Web site: PROSITE
  • Data location: ftp://ftp.expasy.org/databases/prosite/
  • File(s) to download: prosite.dat and prosite.doc
  • Impilo location: /opt/bio/data/prosite
  • EMBOSS indexer: prosextract

• PRINTS : Protein signature database
  • Web site: PRINTS
  • Data location: ftp://ftp.bioinf.man.ac.uk/pub/prints/
  • File(s) to download: prints<version>.dat.gz
  • Impilo location: /opt/bio/data/prints
  • EMBOSS indexer: printextract

• REBASE : Restriction enzyme database
  • Web site: REBASE
  • Data location: ftp://ftp.neb.com/pub/rebase
  • File(s) to download: withrefm.<version> and proto
  • Impilo location: /opt/bio/data/rebase
  • EMBOSS indexer: rebaseextract

EMBOSS uses indexing applications to take the content of the database files and create indexes that other programs can use. A very general procedure uses the following step:

• Get into the appropriate location in /opt/bio/data.

• You need to not only act as root but also be root; acting through sudo is not enough:

% sudo su

• Once you are root, you simply need to call up the appropriate indexer for a given database and follow its instructions! Following indexing, the applications requiring a database should now work as advertised.