BioBit No 19 ( ARCHIE )

"Robert Harper Finland", CSC HARPER at CSC.FI
Wed Mar 20 12:42:00 EST 1991

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                                 No 19
                          BIO-NAUT NEWSLETTER
                     << EDITED BY ROBERT HARPER >>
   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. 
   So how do you get to use ARCHIE? If you are Internet connected, it's
   easy. Telnet to quiche.cs.mcgill.ca ( or and
   login as user "archie".  "help" gets a list of valid commands. 

   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.


   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             ! Opening up the telnet session
Connected to
Escape character is '^X'.
Interrupt remote process character is '^C'.
SunOS UNIX (quiche.CS.McGill.CA)
login: archie                   ! Give archie as username.


  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 **


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 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>
    site col.hp.com


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
  ---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 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.

    list [<regex>]
 will list all sites in the database, while
    list \.de$
 lists all German sites.


   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                        23:07  7 Mar 1991
ltisun.epfl.ch                       21:58  7 Mar 1991
nic.switch.ch                           19:15  7 Mar 1991
siam.unibe.ch                          14:17  7 Mar 1991


   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
  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

 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.

   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

archie> prog dotty
# matches / % database searched:    5 / 96%
Host genbank.bio.net   (
Last updated 23:33  7 Mar 1991
      Location: /pub/mac
      FILE      rw-rw-r--    236829  Aug  2  1989   dottyplot.hqx
      Host menudo.uh.edu   (
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   (
Last updated 23:33  7 Mar 1991
      Location: /pub/mac
      FILE      rw-rw-r--      2965  Oct 26  1989   dottyplot.readme
      Host gatekeeper.dec.com   (
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:-)


   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).


 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


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