ACEDB: A C.elegans Database

	R. Durbin and J. Thierry-Mieg

                            December, 1991.

LIST OF FILES: 

README		brief list of files
NOTES		this file
INSTALL		first time installation script
bin.sparc.n_k	sparc (SUN) executables, run time files, documentation.
bin.mips.n_k	mips (DECstation) executables, etc.
bin.iris.n_k	iris (Silicon Graphics) executables, etc.
source.n_k	the full source directories for remaking acedb, including
		documentation.
update.n-i	update files.  i will range from 1 to m, the current
		database minor version.

	All files except NOTES, README and INSTALL, which will all
also be found in wdoc after installation, are tar.Z files.  They will
be uncompressed and untarred automatically by the INSTALL script if
you are using it to install for the first time.  If you are just
adding an update file then you should do this yourself by going to the
$ACEDB home directory and typing
	zcat xxx.tar.Z | tar xvf -

The major version, n, should agree for all the files that you are
using.  The minor versions for the program (source and bin) and for
the data (database and update's) are different.  update.n-i converts
from database.n-(i-1) to database.n-i. 

		     ******* IMPORTANT ******* 
You only need either bin... or source....  It is simplest to have
bin...  if you are using a Sun sparcstation, Dec Unix workstation
(mips chip) or Silicon Graphics Iris workstation.  You would only need
source... if you are going to recompile, e.g. on a different computer
type (or if you want to look at the code!).

CURRENT STATE OF THE SYSTEM: 
The current state in terms of versions is that n=1, k=6, m=10.  The
contents of the update files are:

1-1 CGC Bibliography and 3-point-data
1-2 CGC 2-point data
1-3 Gene list, Lab list, Gazette and meeting titles, CGC strains
1-4 EMBL worm sequences, ZK637 cosmid, YAC lengths, 1st set of cDNA map
	data, a few miscellaneous alterations
1-5 MRC allele list, CGC genetic map (June 1991).
1-6 Common restricition site list, Physical map (July 14, 1991).
1-7 Phys.Map (29/8/91), first set of cDNA's, cDNA map update, 
	cosmids ZK643 and B0303, changes to old sequence info for 
	new sequence display.
1-8 Phys map (1/11/91), addresses, cosmid F59B2, Vancouver allele
	list, updates and changes to old data.
1-9 Phys map update (19/12/91), 1207 cDNA's (as in Gazette 12 no.2).
1-10 Phys map update (March 5,1992), cDNA's as in the
Nature-Genetics paper (Waterston et al.), the sequence of zk638,
data for the Yac-grids. cgc-map of feb92. Unfortunately, we are late
on the biblio.
1-11 cgc-3p data, embl  dna, wspec corresponding to code 1_7, i.e.
do ftp 1-11 to your site if you cannot install code 1_7

New updates, i.e. update.1-12 etc, will be issued approximately monthly
by placing them in the public ftp sites and sending email to users on
the current users list.

******************************************************************
*** Put yourself on the email mailing list if you want notification
*** of release of updates.  To do this, send mail to 
***	rd@mrc-lmba.cam.ac.uk  or  mieg@frmop11.bitnet
******************************************************************

There is a copyright notice in subdirectory wdoc that says that there
is absolutely no guarantee of any kind, and that we don't mind you
giving acedb away, but we don't want either you, or whoever you give
it to, to try to make money from it.

HOW TO GET THE LATEST RELEASE:
You are welcome to copy acedb from a friend, but if you have access to
internet then it may be best to get your own version to be sure it is
up to date.  The latest version of this program is available by ftp
from several public file servers.  In each case log in as user
"anonymous" and give a user identifier as password.

1) crim.crim.fr (192.54.151.100) in France, directory pub/acedb
2) cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb
3) ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb

An example session would be:

ftp crim.crim.fr
login: anonymous
password: your user id or email address
cd pub/acedb
binary
ls
get README
get NOTES
get INSTALL
get bin.sparc.1_4.tar.Z
get update*
quit

HOW TO INSTALL THE SYSTEM

The INSTALL script works correctly for a new installation or when
just to install the latest release. In the later case, it saves and
restores tha passwd and semaphore files.

A full installation guide is kept in the user guide
$ACEDB/wdoc/installation_guide.tex explaining among other things how to grant
read/write access to the users.  There may also be a postscript version in
installation_guide.PS that you can directly print on your laser printer via
	lpr manual.PS

If you really can't wait to get that, or make it work, then here are
brief instructions.  You should put all the distribution tar.Z files
that you need in a single directory on a disk with at least 40 Mega
bytes free space.  We recommend that this is the home directory of a
new user, ~acedb.  Then run the shell script INSTALL.

source INSTALL

Hopefully, you will obtain the result:

DIRECTORY STRUCTURE 
to be able to run one needs $ACEDB (the home directory) with
subdirectories:

       acedb   # executable file to be moved in /usr/local/bin
       database  
          blocks.wrm	the database
	  ACEDB.wrm	little friend file
       bin		the executable(s).
	  xace
       wspec		application dependent specification files.
	  GraphPackage
          copyright
	  sysclass.wrm
	  systags.wrm
          classes.wrm
	  options.wrm
	  sysoptions.wrm
	  displays.wrm   # You may want to edit this file
	  tags.wrm
	  quovadis.wrm	
	  models.wrm 
	  help.wrm
	  semkey.wrm     # You must probably edit this file
	  passwd.wrm     # and this one
	  disptype.wrm
        wdoc
	  various files including the  instalation_guide.tex
	rawdata
	  update files

Your database directory will be empty if you have not run the
program yet and have not loaded in a premade database (no longer in
the ftp directories).  The files blocks.wrm and ACEDB.wrm will be
made the first time you run the program.  The directory must exist.
Before running the system, each user must set the environment
variable ACEDB to the absolute path to the main ACEDB directory (by
e.g.  "setenv ACEDB ~acedb"), and put the executable in their path.
This is done most easily by moving the shell scripts acedb and
textace prepared by the INSTALL script into /usr/local/bin.

The program is supposed to reconise monochrome and color screens.
This sometimes fail, if you understand why, please let us know.
In case of problem with a black and white screen, try 'setenv MONO',
or alternatively, 'setenv ACEDB_COLOR'. 

On DEC stations, there is a font problem, Jack Leunissen reports
that on his DEC 5000, running ultrix 4.2, you can fix it this way:
        xset +fp ......
        mv fonts.alias-mit fonts.alias (in the MIT font dir)
Also, to recompile on the DEC, add in wh a symbolic link to mit X11:
        cd $ACEDB_SRC/wh ; ln -s /usr/include/mit/X11 X11

An on line help is contained in ${ACEDB}/wspec/help.wrm and is
activated by the help option in the menu, or by function key F1 or
F10, or, on a Sun under twm, the help key.

--------------------------
