Instructions d'installation et de configuration de EMBOSS 6.4.0

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 (for PHYLIP compilation)
• libhpdf-dev
• ant (for Jemboss' Java code compilation)
• libmysqlclient-dev (for MySQL access of ENSEMBL data from EMBOSS)

% apt-get install libx11-dev libgd2-xpm-dev libpng3-dev libpng12-dev libgd-tools libplplot-dev plplot9-driver-gd libxaw7-dev libhpd-2.1.0 libhpd-dev ant libmysqlclient-dev libpam0g-dev

Three important details:

• Be sure to have Sun's JDK6 installed and not JRE6. This is an important difference since JDK 6 is needed to build Java applications; JRE6 can only use to run already built Java apps.

• Since EMBOSS contains wrappers for using clustalw and primer3, make sure that these two apps have been installed.

• The file named /usr/lib/jvm/java-6-sun/include/jni.h has problems… The following line must be changed:
  • Commande:

    sudo vi /usr/lib/jvm/java-6-sun/include/jni.h

  • Ligne avant:

    #include "jni_md.h"''

  • Ligne après:

    #include "linux/jni_md.h"''

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

• The archives for the source code of EMBOSS and EMBASSY applications are downloaded from the web site and decompressed in /home/bioubuntu. Get into the EMBOSS-6.4.0 folder, create another folder called embassy and move into this folder:

% wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz
% tar -zxvf EMBOSS-6.4.0.tar.gz
% cd EMBOSS-6.4.0 
% mkdir embassy
% cd embassy

• The EMBASSY applications can be downloaded from this web site: ftp://emboss.open-bio.org/pub/EMBOSS/. Here is the list of EMBASSY applications included in Impilo:
  • 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/CBSTOOLS-1.0.0.tar.gz
% tar -zxvf CBSTOOLS-1.0.0.tar.gz
#
# Do the samme for all the other EMBASSY applications
#

• The EMBOSS-6.4.0 folder is moved under /opt/bio/sources and should now belong to root. Its permissions should be 755.

% sudo mv ~/EMBOSS-6.4.0 /opt/bio/sources
% sudo chown -R root:root /opt/bio/sources/EMBOSS-6.4.0
% cd /opt/bio/sources/EMBOSS-6.4.0

• The compilation is done using the usual build procedure:

% sudo ./configure --with-x --enable-64 --with-java=/usr/lib/jvm/java-6-sun --with-javaos=/usr/lib/jvm/java-6-sun/include
% sudo make && sudo make install

• Be patient, its is going to take a while… Once the install is done, test it:

% cd
% embossversion
# You should see this:
Reports the current EMBOSS version number
6.4.0.0
%

• On the contrary, if you see this, the solution is simple:

% embossversion
embossversion: error while loading shared libraries: libnucleus.so.6: cannot open shared object file: No such file or directory
# Use this command:
% sudo /sbin/ldconfig

• To use the EMBASSY applications, you will need to go into each and every folder found in embassy and compile the applications manually. For example:

% cd ./embassy/CBSTOOLS-1.0.0
% sudo ./configure --with-x --enable-64 --with-java=/usr/lib/jvm/java-6-sun --with-javaos=/usr/lib/jvm/java-6-sun/include
% sudo make && sudo make install

• Last thing to do is to “fix” the Jemboss startup script. This script is written for the csh shell, not the bash shell, which is Ubuntu's default:

#!/bin/csh
setenv CLASSPATH blablabla...

becomes:

#!/bin/sh
export CLASSPATH=blablabla...

• The installation process places the applications for immediate use. To ease its use, change the way to access the Jemboss script:

% sudo ln -s /usr/local/bin/runJemboss.csh /usr/local/bin/runJemboss

• Pour

• Les applications EMBOSS/EMBASSY sont maintenant disponibles via la ligne de commande. Pour Jemboss, il faut maintenant ajouter l'ajouter dans le menu Impilo > Applications d'usage général:
  • À venir…

• Pour démarrer Jemboss à partir de la ligne de commande:

% 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.