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 |
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%
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 |