2.5. Downloading the Stable Release

2.5.1. Downloading via the EMBOSS Website

The simple way to download a stable release for EMBOSS or an EMBASSY package is, from a web browser, to click on the appropriate links from the EMBOSS website:

http://emboss.open-bio.org

2.5.2. Downloading via Anonymous FTP

Stable releases are available via anonymous FTP. From a terminal prompt, change directory to a location in which to download the source code, then start your FTP client and point it to emboss.open-bio.org :

% ftp
ftp>  open emboss.open-bio.org
Connected to emboss.open-bio.org (207.154.17.70).
220 (vsFTPd 2.0.1)

Anonymous FTP is being used so you must log on using the username anonymous and your IP address as the password:

Name (emboss.open-bio.org:auser): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.

You must change directory to pub using cd pub. If you list (using ls) the directory you will see directories for EMBOSS and various other open source projects (bio*):

ftp> ls
227 Entering Passive Mode (207,154,17,70,160,136)
150 Here comes the directory listing.
drwxr-xr-x    8 14       50           4096 May 22  2006 pub
226 Directory send OK.
ftp> cd pub
250-Test.
250 Directory successfully changed.
ftp> ls
227 Entering Passive Mode (207,154,17,70,170,81)
150 Here comes the directory listing.
drwxrwsr-x   10 501      503          4096 Aug 21 12:17 EMBOSS
drwxrwsr-x    7 528      536          4096 Dec 23  2003 biodas
drwxrwsr-x    4 0        48           4096 May 22  2006 biojava
drwxrwsr-x    4 520      510          4096 Nov 11  2005 bioperl
drwxrwxr-x    4 0        48           4096 May 22  2006 biopython
drwxr-xr-x    2 500      0            4096 Aug 09  2005 scratch
226 Directory send OK.

Move to the EMBOSS directory and list the contents. You will see the various releases and directories:

ftp> cd EMBOSS
250 Directory successfully changed.
ftp> ls
227 Entering Passive Mode (207,154,17,70,78,221)
150 Here comes the directory listing.
-rw-rw-r--    1 501      503        418819 Jul 14  07:54 CBSTOOLS-1.0.0.tar.gz
-rw-rw-r--    1 501      503        437275 Jul 14  07:54 DOMAINATRIX-0.1.0.tar.gz
-rw-rw-r--    1 501      503        448550 Jul 14  07:54 DOMALIGN-0.1.0.tar.gz
-rw-rw-r--    1 501      503        487462 Jul 14  07:54 DOMSEARCH-0.1.0.tar.gz
-rw-rw-r--    1 501      503      84278046 Jul 15  03:53 EMBOSS-6.4.0.tar.gz
.
...  screen output truncated 
.
drwxrwsr-x    2 501      503          4096 Jul 06   2005 tutorials
drwxrwsr-x    3 501      503          4096 Jul 26  09:57 windows
226 Directory send OK.

Now use get to get the file you want. The following example downloads the EMBASSY package TOPO:

ftp> get TOPO-1.0.0.tar.gz
local: TOPO-2.0.0.tar.gz remote: TOPO-2.0.0.tar.gz
227 Entering Passive Mode (207,154,17,70,214,248)
150 Opening BINARY mode data connection for TOPO-2.0.0.tar.gz (411485 bytes).
226 File send OK.
411485 bytes received in 14 seconds (29 Kbytes/s)

Do a get for each file you need, or use mget *gz to download all the files at once. Exit your FTP session with the command quit. List your directory and you'll see you have the file you requested:

ftp> quit
221 Goodbye.
% ls
TOPO-1.0.0.tar.gz
%

2.5.2.1. Unpacking EMBOSS and EMBASSY Packages

The stable release of EMBOSS must be unpacked before installation. Use the gunzip and tar commands to unpack the distribution. The commands needed for EMBOSS Version 6.4.0:

gunzip EMBOSS-6.4.0.tar.gz
tar xvf EMBOSS-6.4.0.tar

The stable release of any EMBASSY packages must also be unpacked before installation. For example, to unpack HMMER-2.3.2):

gunzip HMMER-2.3.2.tar.gz
tar xvf HMMER-2.3.2.tar