To download via CVS you must have cvs installed on your system. It is there if an application is listed after typing:

You must also use the secure shell SSH for the file transfer. Depending on your shell, type one of the following:

To checkout the EMBOSS source code tree, go to the directory where you want the top-level EMBOSS directory created. For example to create EMBOSS in /home/auser/src/ you'd type:

To checkout EMBOSS you must first logon to the open-bio.org CVS server by typing:

You will be prompted for a password which is cvs. You are now logged on to the CVS server. Checkout (download) EMBOSS by typing:

This will take some time as it's downloading several megabytes of source code and data from the USA. Once the download is complete, terminate your CVS session with:

Here is a typical CVS session:

% declare -x CVS_RSH=ssh
% cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/emboss login
Logging in to :pserver:cvs@cvs.open-bio.org:2401/home/repository/emboss
CVS password:
% cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/emboss checkout emboss
cvs checkout: Updating emboss
cvs checkout: Updating emboss/emboss
U emboss/emboss/AUTHORS
U emboss/emboss/COMPAT
U emboss/emboss/COPYING
U emboss/emboss/ChangeLog
.
...  screen output truncated 
.
%
% cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/emboss logout
Logging out of :pserver:cvs@cvs.open-bio.org:2401/home/repository/emboss
%
% ls
emboss  

Once you've downloaded the CVS version of EMBOSS, you should keep up-to-date with the latest changes. To do this, move to the directory which you wish to update (or the root emboss directory to update everything) and type:

Bear in mind that if you have edited any files then those edits will be merged with the version downloaded via CVS. Therefore if you wish to conserve your edits in their original form, you should copy the edited files to a safe place first.

You must first build the script and other files used to configure the package. From the second-level EMBOSS directory (e.g. /home/auser/emboss/emboss) type:

aclocal is part of the automake package. These commands build the "configure" script from the file configure.in (in the EMBOSS distribution) and various other files needed for installation. Specifically:

If you experience any errors at that stage it is possible that your GNU configuration tools are out of date, if so then update them. It is also possible that your version of libtool is more recent than that used in the current EMBOSS CVS; you can check that by looking at the version number in the ltmain.sh file at the top source level of the checked-out tree. If your installed version of libtool is newer then you may have to type autoreconf -fi and then retype the previous GNU configuration tool commands. autoreconf is part of the autoconf package.

Running the resulting ./configure will

./configure is controlled by command line arguments and by environment variables. Command line arguments are generally used to switch on features autoconf was unable to detect. Environment variables are generally used to set build information such as compiler options.

If you intend to compile using make install (see below) you must specify an installation area for the executables and supporting files. It is good practice to specify these even if you intend to compile with a plain make. To do this, type:

./configure --prefix=/home/auser/emboss

Further, if you are using the gcc compiler it's a good idea to turn warnings on (most EMBOSS warnings are bad errors). You can do this while setting the installation areas:

You can also turn on more strict developer warnings by typing:

There is a further configuration switch, --enable-devextrawarnings, which turns on some rather pedantic warnings which are nonetheless useful in some rare circumstances. As that switch can produce compilation noise it is not recommended to specify it in general use.

To compile EMBOSS, type:

This will, by using the Makefiles, compile all the source files into executable binaries within your chosen checked-out location e.g.:

Alternatively, compiling with:

will install the binaries and supporting files into bin, lib and share subdirectories of the directory you specified using --prefix on the configure line. In the example above, this is the top-level emboss directory level from the CVS checkout, e.g.:

Had you not specified --prefix=/home/auser/emboss they'd be installed to /usr/local by default (that isn't recommended).

If you want EMBOSS installed in somewhere other than /usr/local then use the --prefix option of GNU configure to specify the EMBOSS installation directory. This is the recommended method of installation as EMBOSS has hundreds of files which might otherwise obscure other software, particularly under /usr/local/bin.

To compile and reinstall EMBOSS on subsequent occasions, use the following commands:

Though extremely rare, there are circumstances where you may have to type rm config.cache (on very old installations) or rm -rf autom4te.cache before doing the above. Those occasions generally happen when trying to update a rather old existing version of EMBOSS.

You must set the path to the executable applications. Assuming EMBOSS was installed in your home directory and you are using a csh style shell then type the following commands (replace the path as required):

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

If, however, you installed using make install rather than just a make then the commands will be different (you must set the PATH to where you installed the executables). For a csh style shell:

For a sh style shell:

To test all is well with your installation you can run:

and check that you get the EMBOSS version number 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 this however you need to set up the databases for use with EMBOSS.

Database setup is covered in the EMBOSS Administrators Guide); only the bare essentials are covered below.

The EMBOSS distribution comes bundled with some test databases. They are, for example, located in:

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

These files are used to configure EMBOSS. .embossrc is for personal configuration whereas emboss.default is used for site-wide configuration. A template file is included in the CVS releases (.../emboss/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: /home/auser/workspace/emboss/emboss/test/embl/
file: *.dat
comment: "EMBL sequences"
]


DB swissprot
[ 
type: P 
method: direct
format: swiss
dir: /home/auser/workspace/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 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 example below is for installing the CVS (developers) version of an EMBASSY package PackageName.