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No 19
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BIO-NAUT NEWSLETTER
<< EDITED BY ROBERT HARPER >>
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When I go shopping for the family I open up the local newspaper and look
to see if there are any special offers. I go to shops that are
conveniently near and who have the items that I want. There is nothing
more frustrating to travel miles to a shop only to find out that they do
not have the thing that you want in stock.
As you will be well aware there are many "anonymous FTP shops" which
offer a large selection of software and information for downloading. Now
wouldn't it be nice to have a "local newspaper" that you could browse
through and see what was on offer. You might discover some "FTP shop"
close at hand that had just the item that you were looking for. Well
this editon of BioBit gives you and intoduction to ARCHIE... the
ultimate remedey for the ftp blues.
GETTING TO THE POINT.
So how do you get to use ARCHIE? If you are Internet connected, it's
easy. Telnet to quiche.cs.mcgill.ca (132.206.2.3 or 132.206.51.1) and
login as user "archie". "help" gets a list of valid commands.
WHAT ARCHIVE SITES DOES ARCHIE KNOW ABOUT ?
The "list" command allows you to specify a regular expression as an
argument and prints the site names in the database which match that
expression, along with the primary IP address of the site and the date
that ARCHIE last updated the site for the database. "list" without an
argument prints the data on all sites that ARCHIE knows about.
ARCHIE SESSION WITH COMMENTS.
In this session I will go through some of the basic commands just to
show how the system operates. I will take a look at the following
commands (SITE, LIST, PROG, MAIL, EMAIL), that should be enough to give
you a taste of the possibilities. Site allows you to get directories
of a well known FTP site. List helps you to find out more about ftp
sites that may be in your geographical region. Prog helps you to find
out where a particular programme might be kept. Mail allows you to get
the results of your searches sent back to you via mail. And Email is for
the fans of Bitnet who have no Internet access.
$ telnet 132.206.2.3 ! Opening up the telnet session
Trying...
Connected to 132.206.2.3.
Escape character is '^X'.
Interrupt remote process character is '^C'.
SunOS UNIX (quiche.CS.McGill.CA)
login: archie ! Give archie as username.
WELCOMING MESSAGE.
ARCHIE: The McGill School of Computer Science Archive Server [12 Mar 1991]
******* Welcome to ARCHIE Version 2.0 ******
Speed and performance under load should be improved.
3 new searching methods added. See help section under "set search".
Output may now be sorted. See help under "set sortby".
New Software Description database to help you find the names of packages
to do what you want done. See help under "whatis".
New "mail" command allows you to mail ARCHIE results back to you. See
help under "mail" and "set mailto".
A "status" variable allows you to turn on or off search progress
information. Help "set status".
** There is a problem with numbering split letters. Looking into it.
** If you want to add a site to the ARCHIE database or add/correct the
Software Description Database write to archie-admin at cs.mcgill.ca.
** 'help' for help ** bug reports, etc. to archie-l at cs.mcgill.ca **
THE ARCHIE HELP SYSTEM.
archie> help
Help gives you information about various topics, including all the
commands that are available and how to use them. Telling ARCHIE about
your terminal type and size (via the "term" variable) and to use the
pager (via the "pager" variable) is not necessary to use help, but
provides a somewhat nicer interface.
Currently, the available help topics are:
about - a blurb about ARCHIE
bugs - known bugs and undesirable features
email - how to contact the ARCHIE email interface
help - this message
list - list the sites in the ARCHIE database
mail - mail output to a user
nopager - *** use 'unset pager' instead
pager - *** use 'set pager' instead
prog - search the database for a file
quit - exit ARCHIE
set - set a variable
show - display the value of a variable
site - list the files at an archive site
term - *** use 'set term ...' instead
unset - unset a variable
whatis - search for keyword in the software description database
Help topics available:
about bugs email list
mail nopager pager prog
quit regex set show
site term unset whatis
HELP REGARDING SITE.
Help topic? site
The 'site' command allows you to get a full listing of an ftp site in the
ARCHIE database. The output format is similar to that of ftp's long
recursive listing.
The usage is:
site <site-name>
Example:
site col.hp.com
FINDING OUT ABOUT GENBANK WITH SITE COMMAND.
archie> site genbank.bio.net
-rw-rw-r-- 0 Apr 9 1988 .hushlogin
-rwxrwxrwx 3 Oct 2 16:45 Public -> pub
drwxr-xr-x 512 Aug 29 06:49 bin
drwxr-xr-x 512 Oct 2 16:56 dev
drwxr-xr-x 512 Feb 6 1990 etc
-rwxrwxrwx 7 Oct 2 16:45 lib -> usr/lib
drwxrwxr-x 512 Oct 3 19:24 pub
drwxr-xr-x 512 Feb 6 1990 usr
bin:
---x--x--x 131072 May 10 1990 kermit
---x--x--x 12408 Oct 16 1989 ls
---x------ 98304 May 10 1990 sh
---x--x--x 16384 Aug 29 06:49 xfersh
!!!! COMMENTS !!!!
ARCHIE then begins to give you a listing of all the files at the Genbank
anonymous ftp site, as you can imagine this is LONG so I have edited it
down to root and bin. So you can readily get a listing of all the files
held at Genbank... without going to Genbank to get them.
HELP REGARDING LIST.
Help topic? list
'list' provides a list of the sites in the database and the time at
which they were last updated. There is an optional regular expression
argument to limit the list to specific sites.
Note that the numerical (IP) address associated with a site name is
valid at the listed time, but since they do occasionally change, it is
possible that a discrepancy may occur until that site is updated in our
database. Furthermore, the listed IP address is the primary, as listed
in the DNS database: secondary addresses are not stored.
Usage:
list [<regex>]
Examples:
list
will list all sites in the database, while
list \.de$
lists all German sites.
FINDING OUT ABOUT FTP SITES IN YOUR COUNTRY.
When you go shopping it is usually most convenient to visit the local
shop so if I were from Switzerland I could find out the Swiss FTP sites
by giving the following command. Hmmmm... it looks like ARCHIE does not
know about bioftp.unibas.ch. Well nothing is ever perfect. If your FTP
site is not on ARCHIE and if you want to belong to the ARCHIE database
then you should contact archie-admin at cs.mcgill.ca
archie> list \.ch$
4 currently stored site names match '\.ch$'
iamsun.unibe.ch 130.92.64.10 23:07 7 Mar 1991
ltisun.epfl.ch 128.178.119.94 21:58 7 Mar 1991
nic.switch.ch 130.59.1.40 19:15 7 Mar 1991
siam.unibe.ch 130.92.66.11 14:17 7 Mar 1991
HELP REGARDING PROG.
Site and List are rather broad spectrum commands, and they give you the
big picture of what is going on in the FTP world, but very often you are
only interested in locating a specific programme that you have heard
a whisper about on BIO-SOFTWARE. The Prog command helps you to locate it.
Help topic? prog
The 'prog' command allows you to search the database for a specified
pattern.
The usage is:
prog <expression>
where the interpretation of <expression> depends on the current value of
the 'search' variable. Searches may be performed in a number of
different ways. See the help section on the 'search' variable for a full
explanation.
The output of prog can be sorted in different ways, depending on the
value of the 'sortby' variable. See help for the 'sortby' variable for a
full explanation.
FINDING OUT WHERE A CERTAIN PROGRAMME IS KEPT.
Now I know that dottyplot is kept at Huston and Indiana, and since dotty
is such a nice string I can ask ARCHIE to tell me which FTP sites it is
available from. ARCHIE will reply by telling you the number of hits,
the host where the software is kept, and the exact location of the
directory. This feature is most likey the best invention since sliced
bread:-)
archie> prog dotty
# matches / % database searched: 5 / 96%
Host genbank.bio.net (134.172.1.160)
Last updated 23:33 7 Mar 1991
Location: /pub/mac
FILE rw-rw-r-- 236829 Aug 2 1989 dottyplot.hqx
Host menudo.uh.edu (129.7.1.6)
Last updated 20:17 7 Mar 1991
Location: /pub/genbank-server/mac
FILE rw-r--r-- 236829 Sep 13 20:22 dottyplot.hqx
FILE rw-r--r-- 3713 Sep 13 20:22 dottyplot.read
Host genbank.bio.net (134.172.1.160)
Last updated 23:33 7 Mar 1991
Location: /pub/mac
FILE rw-rw-r-- 2965 Oct 26 1989 dottyplot.readme
Host gatekeeper.dec.com (16.1.0.2)
Last updated 14:12 8 Mar 1991
Location: /micro/amiga/fish/ff001
FILE r--r--r-- 11897 Aug 17 15:17 dotty.zoo
!!!!! COMMENTS !!!!!!
As you can see the search comes up with 5 hits. Huston and Genbank
score but Indiana is missing so it looks like Don Gilbert's server is
not in the ARCHIE database. For that matter "the number one FTP site
in the Galaxy" is not in the database either:-)
HELP REGARDING MAIL.
Now it might be that you can not capture all the information that is
given out by ARCHIE... and believe me there is alot of information if
you run a "site" command on your favourite FTP site. In which case there
is a mail option so that the output will be return to you by mail.
help topic? mail
The 'mail' command has two forms:
mail <e-mail-address>[,<e-mail-address2>...]
which causes the output of the last command to be mailed to the
specified address (or comma-separated list of addresses).
mail
which causes the output to be sent to the address specified in the "mailto"
variable. All the various Internet addressing styles are understood.
BITNET sites should use the convention
user at sitename.bitnet
UUCP address can be specified as
