2.7. Installation

Only very basic information on EMBOSS installation is included here. For complete installation instructions see the EMBOSS Administrators Guide.

2.7.1. Overview of the Installation Process

You must first download the EMBOSS source code (see Section 2.5, “Downloading the Stable Release”). The basic installation steps are then:

  1. Configure EMBOSS. The stable release contains a 'configure' script for this.

  2. Compile EMBOSS. This will generate the executable files from the application source code.

  3. Set the PATH to the executables.

  4. Test the installation.

  5. Setting up the installation, including databases you wish to use.

These steps are described in detail below for the EMBOSS stable.

2.7.2. Configuration

You must first run the 'configure' script to configure the package. This can be done by typing the following from the directory EMBOSS was downloaded into (e.g. .../EMBOSS-6.4.0/):


./configure is controlled by command line arguments and by environment variables which are generally used to set build information such as compiler options. If you intend to compiling make install (see below) then you should specify an installation area for the executables and supporting files. It is however good practice to specify these even if you intend to compile with a plain make. So, instead of typing ./configure type:

./configure --prefix=/usr/local/emboss

Running the 'configure' script will

  • Configure your system. For example, the installation path (/usr/local/emboss above) is set and various system variables are set and files are flagged to compile (or not). You need not concern yourself with these details.

  • Check whether your system has the necessary functionality and libraries to compile EMBOSS.

  • Read Makefile.in and generate platform-specific Makefiles that are used later when compiling the package.

If an installation directory is specified then it will be created automatically as long as you have permission to write into the parent directory. Otherwise this directory must be created manually by a user with privilege and ownership adjusted to the username of the EMBOSS installer e.g. :

mkdir /usr/local/emboss
chown auser /usr/local/emboss

The above commands would log you on as 'superuser', a user with special privileges that can do more things than a standard user. After creating a directory, ownership is assigned to the user auser.

2.7.3. Compilation

To compile EMBOSS, type:


from the directory you invoked the configure command.

This will compile the EMBOSS libraries (ajax, nucleus etc.) and then the applications.

Optionally, you may install the libraries and applications to the directory you specified using the --prefix option to the configure command. This is done using:

make install

Files are installed as follows:

  • Binaries (/usr/local/emboss/bin)

  • Shared libraries (/usr/local/emboss/lib)

  • System wide data (/usr/local/emboss/share/EMBOSS/data)

  • Application ACD files (/usr/local/emboss/share/EMBOSS/acd)

  • Documentation (/usr/local/emboss/share/EMBOSS/doc)

  • Test databases (/usr/local/emboss/test)


EMBOSS can be compiled by using the commands make or make install. If you use make install you must specify an installation area for the executables and supporting files (see above). make install may be issed alone or after a make command. If you do not compile by first typing make, then make install will perform both the compilation and installation. It is recommended that you perform compilation and installation separately however as this helps to detect where any failures may have happened.

2.7.4. Setting your PATH


Your PATH is an environment variable that defines a list of directories that the operating system searches to find executable applications in response to a Unix command. For example, when you type a command such as cd or ls the invoked application is (typically) /bin/cd or /bin/ls. Most Unix installations will have put the directory /bin in your PATH automatically. For EMBOSS, you must set the PATH to its executables manually.

You must now set the PATH to include the EMBOSS applications. Assuming EMBOSS was installed in your home directory (e.g. /home/auser/EMBOSS-6.4.0 and you have typed make but not make install, then set the PATH as follows. If you are using a csh style shell type the following commands:

set path=(home/auser/EMBOSS-6.4.0/emboss $path)

Or, if you are using a sh style shell then type the following commands:

export PATH=home/auser/EMBOSS-6.4.0/emboss:$PATH

If, however, you installed using make install rather than just a make then you must set the PATH as follows. For csh style shell:

set path=(usr/local/emboss/bin/ $path)

Or, for a sh style shell:

export PATH=/usr/local/emboss/bin/:$PATH

2.7.5. Testing all is Well

To test all is well with your installation you can run


and check that the EMBOSS version number is reported.

You could also try using the seqret application to retrieve some sequences from the test databases that come bundled with the EMBOSS distribution. Before you can do that you will need to set up the databases for use with EMBOSS.

2.7.6. Database Setup

The setting up of databases is covered in detail elsewhere (see the EMBOSS Administrators Guide), but all you need to know for now is given below.

The EMBOSS distribution comes bundled with some test databases, located in e.g.:


Any database you want to use must be defined in one of the files:

  • .embossrc (in your home directory)

  • emboss.default (in the top-level emboss directory, e.g. /usr/local/emboss/emboss.default)

These files are used to configure EMBOSS. emboss.default is used for site-wide configuration and .embossrc for personal configuration. A template file is included in the stable release (.../share/EMBOSS/emboss.default.template). For now, create a file called .embossrc in your home directory with the following contents (you'll need to change the paths to the test directories):

DB embl 
type: N 
method: direct
format: embl
dir: usr/local/emboss/emboss/test/embl/
file: *.dat
comment: "EMBL sequences"

DB swissprot
type: P 
method: direct
format: swiss
dir: usr/local/emboss/emboss/test/swiss/
file: seq.dat
comment: "Swissprot sequences"

Having set up your databases, issue the following commands (and accept the default values at the prompts):

seqret embl:x65923
more x65923.fasta
seqret swissprot:UBR5_RAT
more UBR5_RAT

If you get output similar to the following then you can rest assured that the installation went well.

% seqret embl:x65923
Reads and writes (returns) sequences
Output sequence [x65923.fasta]:

% more x65923.fasta
>X65923 X65923.1 H.sapiens fau mRNA


% seqret swissprot:UBR5_RAT
Reads and writes (returns) sequences
Output sequence [ubr5_rat.fasta]:

% more ubr5_rat.fasta
>UBR5_RAT Q62671 E3 ubiquitin-protein ligase UBR5 (6.3.2.-)

2.7.7. Installing EMBASSY Packages

The examples below are for installing an EMBASSY package PackageName. It is assumed that you have uncompressed the package (gunzip PackageName.tar.gz) and extracted it (tar xvf PackageName.tar). Stable Release

If you configured EMBOSS using a 'prefix' e.g.:

./configure --prefix=/usr/local/emboss

and followed this with:

make install

which is highly recommended, then:

  1. Go into the PackageName directory:

    cd PackageName
  2. Configure the EMBASSY package using the same options you used for the main package, e.g.:

    ./configure --prefix=/usr/local/emboss --with-pngdriver=/opt/lib

    for the main package then use the same command for the EMBASSY package.

  3. Compile the package:

    make install

If you configured EMBOSS without using a prefix and followed that with make install or specified a prefix of /usr/local (which amounts to the same thing) then the instructions are the same as above except you must configure using (e.g.):

./configure --prefix=/usr/local --with-pngdriver=/fu/bar --enable-localforce

Note the use of the --enable-localforce switch.

If, on the other hand, you did not compile EMBOSS using make install:

  1. Go to the emboss directory:

    cd EMBOSS-6.4.0
  2. Make new directory embassy if it does not exist already:

    mkdir embassy
  3. Go into that directory:

    cd embassy
  4. Decompress and unpack the file:

    gunzip PackageName.tar.gz
    tar xvf PackageName.tar
  5. Go into the PackageName directory:

    cd PackageName
  6. Configuration should be done using the same options you used for the main EMBOSS package. So, if you used:

    ./configure --with-pngdriver=/fu/bar

    for the main package then use the same command for the embassy package.

  7. To compile: