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

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

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:

Running the 'configure' script will

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. :

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.

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:

Files are installed as follows:

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:

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

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

Or, for a sh style shell:

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.

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:

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):

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
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

%

% 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.-)
MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTLDT
PQLERKRTRELLELGIDNEDSEHENDDDTSQSATLNDKDDESLPAETGQNHPFFRRSDSM
TFLGCIPPNPFEVPLAEAIPLADQPHLLQPNARKEDLFGRPSQGLYSSSAGSGKCLVEVT
MDRNCLEVLPTKMSYAANLKNVMNMQNRQKKAGEDQSMLAEEADSSKPGPSAHDVAAQLK
SSLLAEIGLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGAEPG
SILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCAT
TPMAVHRVKVTFKDEPGEGSGVARSFYTAIAQAFLSNEKLPNLDCIQNANKGTHTSLMQR
LRNRGERDREREREREMRRSSGLRAGSRRDRDRDFRRQLSIDTRPFRPASEGNPSDDPDP
LPAHRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI
VAHGRENGADSILDLGLLDSSEKVQENRKRHGSSRSVVDMDLDDTDDGDDNAPLFYQPGK
RGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKVLLGRKVNWHDFAF
FDPVMYESLRQLILASQSSDADAVFSAMDLAFAVDLCKEEGGGQVELIPNGVNIPVTPQN
VYEYVRKYAEHRMLVVAEQPLHAMRKGLLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQML
ISFTSFNDESGENAEKLLQFKRWFWSIVERMSMTERQDLVYFWTSSPSLPASEEGFQPMP
SITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIKTKNFGFV

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).