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 :
%ftpftp>open emboss.open-bio.orgConnected 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):anonymous331 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>ls227 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 pub250-Test. 250 Directory successfully changed.ftp>ls227 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 EMBOSS250 Directory successfully changed.ftp>ls227 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.gzlocal: 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>quit221 Goodbye.%lsTOPO-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 |