1.1. Downloading EMBOSS

1.1.1. Downloading with a Web Browser

You should use the URL:


The file you need for the EMBOSS base installation is


This will always be a link to the most recent version of EMBOSS. In the example given it is a link to EMBOSS-6.0.1.tar.gz. The other gz files are the EMBOSS-associated EMBASSY packages. These are extra files you can apply to the base EMBOSS installation. The EMBASSY packages are dealt with in a separate section of this book: you can download these optional files at the same time as EMBOSS-latest.tar.gz if you intend installing them.

1.1.2. Downloading by Anonymous FTP Interactive FTP

Change directory to the location in which you wish to download the source code. In this example you will download the source to /usr/local/src/EMBOSS. Then start your FTP client and point it to emboss.open-bio.org.

% ftp emboss.open-bio.org
Connected to emboss.open-bio.org (
220 (vsFTPd 2.0.1)
Name (emboss.open-bio.org:username):

The FTP server uses anonymous FTP so type in the username anonymous.

Name (emboss.open-bio.org:username):anonymous
331 Please specify the password.

Enter your email address here as the password for user anonymous. You could, in fact, type anything but it is a common courtesy to use your email address so the developers can get some idea of which sites have downloaded the software. Your email address will only be used for gathering such statistics. The FTP server will respond with something similar to the following:

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.

You should now set your FTP client to use passive mode. How to do so depends on your FTP client. It is usually done by using the command passive or the command pasv; sometimes the FTP client has no such command and will usually already be in passive mode. To find out which, if any, command to type you can use the help command to show which commands your FTP client supports.

Commands may be abbreviated.  Commands are:
!               cr              mdir            proxy           send
$               delete          mget            sendport        site
account         debug           mkdir           put             size
append          dir             mls             pwd             status
ascii           disconnect      mode            quit            struct
bell            form            modtime         quote           system
binary          get             mput            recv            sunique
bye             glob            newer           reget           tenex
case            hash            nmap            rstatus         trace
ccc             help            nlist           rhelp           type
cd              idle            ntrans          rename          user
cdup            image           open            reset           umask
chmod           lcd             passive         restart         verbose
clear           ls              private         rmdir           ?
close           macdef          prompt          runique
cprotect        mdelete         protect         safe

In this case the command needed is passive.

Passive mode 

If the server replies with Passive mode off then you were already in passive mode. In that case type passive again to make sure passive mode is on.

Now move to the directory containing the EMBOSS source code files and list the contents of that directory.

ftp> cd /pub/EMBOSS
250 Directory successfully changed.
227 Entering Passive Mode (209,59,5,172,27,195)
150 Here comes the directory listing.
-rw-rw-r--    1 501      503        343812 Jul 15 19:45 CBSTOOLS-1.0.0.tar.gz
-rw-rw-r--    1 501      503        420983 Jul 15 19:45 DOMAINATRIX-0.1.0.tar.gz
-rw-rw-r--    1 501      503        462156 Jul 15 19:45 DOMALIGN-0.1.0.tar.gz
-rw-rw-r--    1 501      503        470537 Jul 15 19:45 DOMSEARCH-0.1.0.tar.gz
-rw-rw-r--    1 501      503      20204153 Jul 16 18:48 EMBOSS-6.0.1.tar.gz
lrwxrwxrwx    1 501      503            19 Jul 16 19:05 EMBOSS-latest.tar.gz -> EMBOSS-6.0.1.tar.gz
-rw-rw-r--    1 501      503        390229 Jul 15 19:45 EMNU-1.05.tar.gz
-rw-rw-r--    1 501      503        431898 Jul 15 19:45 ESIM4-1.0.0.tar.gz
-rw-rw-r--    1 501      503        565686 Jul 15 19:45 HMMER-2.3.2.tar.gz
-rw-rw-r--    1 501      503        339939 Jul 15 19:45 IPRSCAN-4.3.1.tar.gz
drwxrwsr-x    7 501      503          4096 Feb 01  2006 Jemboss
-rw-rw-r--    1 501      503        450102 Jul 15 19:45 MEMENEW-0.1.0.tar.gz
-rw-rw-r--    1 501      503        365566 Jul 15 19:45 MIRA-2.8.2.tar.gz
-rw-rw-r--    1 501      503        445562 Jul 15 19:45 MSE-1.0.0.tar.gz
-rw-rw-r--    1 501      503        343305 Jul 15 19:45 MYEMBOSS-6.0.0.tar.gz
-rw-rw-r--    1 501      503        374766 Jul 15 19:45 MYEMBOSSDEMO-6.0.0.tar.gz
-rw-rw-r--    1 501      503       1624802 Jul 15 19:45 PHYLIPNEW-3.67.tar.gz
-rw-rw-r--    1 501      503        574940 Jul 15 19:45 SIGNATURE-0.1.0.tar.gz
-rw-rw-r--    1 501      503        532035 Jul 15 19:45 STRUCTURE-0.1.0.tar.gz
-rw-rw-r--    1 501      503        379929 Jul 15 19:45 TOPO-1.0.0.tar.gz
-rw-rw-r--    1 501      503        682200 Jul 15 19:45 VIENNA-1.7.2.tar.gz
drwxrwsr-x    3 522      503          4096 Aug 21  2006 contrib
drwxrwsr-x    2 501      503          4096 Nov 11  2005 doc
drwxrwsr-x    3 501      503          4096 Dec 15 10:41 fixes
drwxrwsr-x   10 501      503          4096 Jul 16 19:00 old
drwxrwsr-x    2 501      503          4096 Jul 06  2005 tutorials
drwxrwsr-x    3 501      503          4096 Jul 16 19:04 windows
226 Directory send OK.

It is essential that you transfer these files as binary. The help command above shows that the command to achieve this is binary, so type it:

200 Switching to Binary mode.

Now download the source gz files.

ftp> get EMBOSS-latest.tar.gz
local: EMBOSS-latest.tar.gz remote: EMBOSS-latest.tar.gz
227 Entering Passive Mode (209,59,5,172,132,86)
150 Opening BINARY mode data connection for EMBOSS-latest.tar.gz (20204153 bytes).
226 File send OK.
20204153 bytes received in 67 seconds (2.4e+02 Kbytes/s)

The file EMBOSS-latest.tar.gz is a link on the FTP server which points to the latest version of the EMBOSS source code. The directory listing from the ls command shows that, in this example, it points to EMBOSS-6.0.1.tar,gz. So, what you've really downloaded is the EMBOSS 6.0.1 source code. The remaining gz files shown in the directory listing are the EMBASSY packages; these are EMBOSS-associated packages which you can optionally install once EMBOSS itself has been installed. If you intend installing the EMBASSY packages then now is a good time to get them too.

If you wish, you can download all the gz files using a single command as long as you set the server to turn prompting off. To do this use the prompt command

ftp> prompt
Interactive mode off

If, instead, the server responded with Interactive mode on, then the server already had prompting turned off; in that case type prompt again.

You can now download all the gz files using mget *gz. Note, however, that this will download both EMBOSS-latest.tar.gz and EMBOSS-6.0.1.tar.gz so there will be some unnecessary bandwidth used.

ftp> mget *gz
local: DOMAINATRIX-0.1.0.tar.gz remote: DOMAINATRIX-0.1.0.tar.gz
227 Entering Passive Mode (209,59,5,172,250,142)
150 Opening BINARY mode data connection for DOMAINATRIX-0.1.0.tar.gz 
(349882 bytes).
226 File send OK.
349882 bytes received in 1.7 seconds (2e+02 Kbytes/s)
local: DOMALIGN-0.1.0.tar.gz remote: DOMALIGN-0.1.0.tar.gz
227 Entering Passive Mode (209,59,5,172,180,127)
150 Opening BINARY mode data connection for DOMALIGN-0.1.0.tar.gz 
(347672 bytes).
. output truncated for clarity

You can now exit from your FTP session with the command quit. FTP using wget

The program wget can be used to download a remote directory non-interactively. More details on wget can be obtained from the Free Software Foundation (http://www.gnu.org). Assuming you have wget installed, use the following command; it will generate a lot of output on the screen:

% wget -m 'ftp://emboss.open-bio.org/pub/EMBOSS/'

--13:46:53--  ftp://emboss.open-bio.org/pub/EMBOSS/
           => `emboss.open-bio.org/pub/EMBOSS/.listing'
Resolving emboss.open-bio.org...
Connecting to emboss.open-bio.org||:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD /pub/EMBOSS ... done.
==> PASV ... done.    ==> LIST ... done.

    [ <=>                                 ] 1,501         --.--K/s

13:46:57 (171.74 KB/s) - `emboss.open-bio.org/pub/EMBOSS/.listing' 
saved [1501]

--13:46:57--  ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-
           => `emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz'
==> CWD /pub/EMBOSS ... done.
==> PASV ... done.    ==> RETR DOMAINATRIX-0.1.0.tar.gz ... done.
Length: 349,882 (342K)
. output truncated for clarity

This command will have created a directory called emboss.open-bio.org/pub/EMBOSS and downloaded the gz files into that directory. Experienced UNIX users may take the opportunity to make a symbolic link called EMBOSS to this directory although it is not, of course, essential.

1.1.3. Unpacking the Source Code

You will have downloaded the EMBOSS source code to a suitable directory. Move to whichever directory you chose (e.g. cd /usr/local/src/emboss) and list the directory to make sure. We'll ignore the EMBASSY packages for now; they are described elsewhere in this book and, besides, you need to install EMBOSS before installing any EMBASSY package.

% ls

The EMBOSS-latest.tar.gz file is a compressed binary file and requires that your UNIX distribution has the gunzip program installed. Check that the command:

which gunzip

gives a positive response. If not then install the gzip package from whichever freeware site your UNIX distribution uses or, alternatively, compile the source code from the gzip homepage (http://www.gzip.org) which contains compilation instructions.

You unpack the EMBOSS distribution by typing:

gunzip EMBOSS-latest.tar.gz

This will create a file called EMBOSS-latest.tar. Such tar files are archive files containing the individual source code files.

You must now extract the archive using the tar program:

tar xf EMBOSS-latest.tar

This will create a new directory, EMBOSS-6.0.1: the exact name will depend on the version of EMBOSS being unpacked. Enter the directory and type ls to show the files. The directory listing should look something like this:

% cd EMBOSS-6.0.1
% ls
. output truncated for clarity

if it doesn't then you're in the wrong directory. You are now ready to configure EMBOSS.


The tar program on most UNIX distributions will usually perform satisfactorily, however some will not. So, check the platform specific notes (Section 1.7, “EMBOSS Installation: Platform-specific Concerns”) to see whether you need to install the GNU version of the tar program instead.