README for acedb source code. -- The code is GPL If you use the acedb_ncbi code please quote AceView: a comprehensive cDNA-supported gene and transcripts annotation, Danielle Thierry-Mieg and Jean Thierry-Mieg Genome Biology 2006, 7(Suppl 1):S12 http://genomebiology.com/2006/7/S1/S12 LINUX: To compile acedb, you must first install the development packages (with header files) for libXaw, libXt, libXmu, libXext and libX11. For example on Fedora, RHEL, CentOS and friends these are named libXaw-devel etc... On Debian based systems (including Ubuntu) they are named eg libxaw-headers. There is a tar file wh/x11.include.tar.gz that you could use if you cannot obtain the headers, but these canned headers may not be exactly in suynch with your X11 libraries -- The documentation is available at https://github.com/jtmieg/AceView/blob/master/acedb_query_language_documentation.pdf -- wdoc	contains many documentation files whelp	contains help files used by the compiled programs. idoc	internal documentation written by Mark S Quick guide to building the system --	% ln -s wmake/makefile .	% make	it will show you the possible machine configurations in sh or bash (linux default shell): % export ACEDB_MACHINE=LINUX_X86_64_4_OPT alternatively in csh or tcsh:	% setenv ACEDB_MACHINE SOLARIS_4 Use the right configuration for your machine. frequent choices are:	SOLARIS_4	any version of solaris	SOLARIS_4_OPT	any version of solaris	LINUX_4	any version of linux LINUX_4_OPT optimized code for linux 32 bits LINUX_X86_64_4_OPT optimized code linux 64 bit	The 4 refers to Acebd version 4, there are many other machines predefined in directory wmake (ALPHA,IBM,SGI etc). If your machine is not listed please prepare a new file wmake/MACHINE_DEF and mail it to mieg@ncbi.nlm.nih.gov I will include it in the distrib, but (in priciple) never edit the machine independant makefile: wmake/truemake On some machines, the optimized version mishandles the color table and the graphic program 'xace' 'xacembly' pops up in grey tones. If this	happens, try the non-optimized graphic code. There is no known optimization bug affecting the non graphic programs.	% make -k all Notice that all object modules and all executable are created in the directory bin.$ACEDB_MACHINE, so you can compile for several platform in parallel.	please use 'make -k all'	the purpose of -k option is to continue compiling	if one of the target fails. For example under my	instalation of CYGWIN, i fail to compile the	rpc 'aceserver' program, because i cannot locate	xdr_free in /usr/lib. But this is immaterial since	the tcp 'taceserver' program, which has equivalent	functionalities compiles and runs.	% cd demo	% sh test_note toto	This will create a tiny database in directory toto	% ../bin*/xace toto	This should open the X11 graphic xacembly code	click on the sequence class, then on one of the	sequences in the main-keyset window, then on the	DNA button in the sequence window	The database is quasi empty, but this is a test	that the whole code runs ok	Click Exit in the main window	% cd ../wac	Look at the README in this directory, it contains the	test suite for the client server system	Notice that acedb supports 3 protocols,	rpc/sanger-tcp/ncbi-tcp	AceView uses ncbi-tcp which is way faster, AcePerl	supports rpc and sanger-tcp	some machines, in particular windows do not support	rpc	To use AcePerl on LINUX ise the rpc method What is here -- demo	a script to create a small demo database - useful to developers	working on the database system, not necessarily useful for	anyone else idoc	Mark Sienkiewicz wrote this documentation while learning the system. w1	tools - basic libraries	[ ace 9 has different message passing (eg. messout, fn names) ] w2	graphics libraries - ps, gif, x11, mac	[ different in ace 9 - gtk ] w4,5	database kernel w6	object layer	universal graphics - keyset display, tree display, few others	dna, peptide w7	biology graphics code	[ quite out of sync with ace 9 - merge is difficult: both have	new features ] w8, wabi	acembly layer	[ not synchronized with ace 9 - we have features they do not have ] w9	high layer tools from sanger: dotter, other wabi	Acembly code to analyse and display sequencing projects and Solexa data wac	AceC : C language programmers interface to acedb The directory contains a test suite	AceC code can run standalone or connect to a distant server	which can be the taceserver or tgifacemblyserver which	are part of this package, or the saceserver which is	part of the sanger acedb code and runs at CSHL wacext	Contains many application code written in AceC	some are used frequently, some are one time shots	and a few are broken, but are not used elesewhere.	cd wacext ; make -k all wace	obsolete tools for importing data wacec	obsolete vahan's ace c library kept for compatibility waction	obsolete - export data, run ext program, reload data	never worked on all platforms wbql	AQL (Acedb Query Language) code, documentation and demo	Having compiled the program (make -k all)	type the command tcsh wbql/bqltest.tcsh	the expected message is: ALL TESTS ARE SUCCESSFUL	otherwise please mail mieg@ncbi.nlm.nih.gov	The documentation is available at https://github.com/jtmieg/AceView/blob/master/acedb_query_language_documentation.pdf wc	examples using ace c wdce	windows RPC - DCE	from Richard II wdnasearch	will be dna search someday wdoc	documentation wext	code that uses acelib	acelib is client library for applications to use - works only	from disk. some of this code used in production wfiche	vahan's biology code - linked to our schema wgd	library that creates gif images wgf	gene finder data tables	gene finder does "a priori gene finding" wgnbk	old program to index and re-export pieces of a large file wh	most include files whelp	online help (html) whooks	schemas and classes that are known intrisicially by the c code wjo	contributed biology graphic code wmake	all makefiles live here wmd5	MD5 hash wnq	"new query" recent tools (library) should be in w1 wquery	place to store standard queries - distributed with system	often out of sync with schema	obsolete? wrpc	rpc client and server code wscripts	external code that we use - see wtools wsocket7	new socket server client (2 versions)	[ was copied from ace 9, but doesn't work for us. ] wspec	standard wspec for creating new database	contains standard worm schema	- should have a minimum schema, or schema with everything the	code knows. wstaden	code borrowed from roger staden - library to read "abi traces"	localized for acedb wtools	external code that we use - see wscripts	schema checker in python	genbank to ace translator wvsim	vahan's general library - like w1	do not use	we keep it for back compatibility so some applications