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 (5/3/92), cDNA's as in the Nature-Genetics paper (Waterston et al.), cosmids ZK638 and R107, data for the Yac-grids, cgc-map of feb92. Unfortunately, our bibliography is still out of date. 1-11 Phys map update (24/4/92), cgc-3p data, EMBL dna update, wspec corresponding to code 1_7, i.e. preserve your old wspec/* if you cannot install code 1_7.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. --------------------------