2004-06-06  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/ACD: adapted to EMBOSS 2.8 (changes in parser, as usual)
	* Xml/: EMBOSS 2.8 

2004-05-30  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/cosa.xml: new program interface (T. Rose)

2004-05-18  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/*.xml: Remove obsolete sptrnrdb databank, now replaced by
	uniprot (Universal Protein Resource).

2004-05-06  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-index.pl: Marc Warmoes Pise index generator (slightly
	adapted).
	* Makefile: added targets for makeindex.
	* Images/: added some files for the index.
	* Xml/: added categories to many files.

2004-05-03  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/service_down.pl: added a case for closing programs using
	databanks.

2004-04-21  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/mfold.xml: Add *.ps files to the Results filenames list.

2004-04-04  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/melting.xml: bug fixes (scale, variable name in 2 parts,...).

2004-02-20  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/plotcon.xml: Correct and simplify the Results filenames list. 

2004-02-16  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/RepeatMasker.xml: Remove obsolete `-id' flag.

2004-01-30  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/cap3.xml: Cap (version 3) is renamed cap3, not to make
	confusion with cap4.

2004-01-28  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/lvb.xml: Create new interface lvb.xml for lvb version 2.1
	Previous one is renamed lvb.xml.1-0

2003-12-30  Nicolas  Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl: System calls fail if interrupted by a
	signal. Duplicate `flock' call to be safe, and remain locked for
	long jobs (This is a *BIG* HACK !).

2003-12-11  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-bioperl.pl, Makefile: remove of old bioperl modules.

2003-12-09  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/seqclean.xml: addition of a new program interface by
	Marc.Logghe@devgen.com 

2003-11-27  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: with_piped_file error in variables escaping

2003-11-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/tipdate.xml: parameter glitches?

2003-11-12  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: spelling error
	
2003-11-03  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Python/Pise/__init__.py: bug fix in _submit, Float type was
	missing in possible data types.

2003-10-27  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/cancel_job.pl: added code to (optionally) directly do the
	qdel/qsig (if PBS) instead of sending an email to the staff (code
	written by Eric Deveaud)

2003-10-22  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: piped_programs now sort the list of programs.

2003-10-20  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl, lib/batch.pl: Control of submissions for PBS
	jobs: whenever a given number of jobs in PBS queues is reached,
	the request is rejected, with an explanation message and a list of
	alternative similar services.
	* lib/mirrors.pl: list of alternative similar services for a given
	program. 
	* Maker/make-cgi.pl: qdel replaced by qsig (qsig cancels a job during
	execution whereas qdel cancel a job waiting in a queue). 

2003-10-15  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/mfold.xml: Format fasta for multiple sequences was not
	correctly read. I take away this option to let work the external 
	reformatter.

2003-09-23  Nicolas  Joly  <njoly@pasteur.fr>

	* Makefile.global: Do not install GIBBS programs.

2003-08-29  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: fixed the url of the XHTML DTD (the wrong url
	seems to be a problem for the Python xml.sax.handler in the
	Pise/Python API.

2003-08-25  Bernard Caudron  <caudron@pasteur.fr>

	* Xml/mfold.xml: version update (3.1.2)

2003-08-19  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/druid.xml: prompt changed for sequences (DNA only)

2003-08-05  Catherine  Letondal  <letondal@pasteur.fr>

	* url of Pise changed to:
	http://www.pasteur.fr/recherche/unites/sis/Pise/
	* Xml/sig.xml: new program for multiple pattern search
	* Maker/make-html-utils.pl, Maker/make-cgi.pl: Pise url change
	reported 

2003-07-17  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/golden.xml: New paragraph for output format.

2003-06-28  Catherine  Letondal  <letondal@pasteur.fr>

	* Makefile.global: added a comment regarding the 
	include Makefile.bioperl statement

2003-06-21  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/fitch.xml: bug fixes (continued)

2003-06-19  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/fitch.xml: bug fixes (consensus tree option and result files)

2003-06-05  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml: EMBOSS files for version 2.6.
	* Xml/dnapars.xml, Xml/protpars.xml: outgroup specified to
	consense as well when specified for protpars.
	
2003-05-27  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/quicktree.xml: Added extra matrix/alignment check, cannot
	handle both at the same time.

2003-05-21  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-real-bioperl.pl: added SYNOPSIS, COPYRIGHT, SEE ALSO
	sections; removed Paragraph and Results parameters from the
	parameter list provided in the DESCRIPION section. Also changed
	the -remote parameter to -location in example.
	* Bio/Tools/Run/PiseJob.pm, Bio/Tools/Run/PiseApplication.pm,
	Bio/Tools/Run/AnalysisFactory/Pise.pm: added SYNOPSIS, COPYRIGHT,
	SEE ALSO sections; changed the -remote parameter to -location.
	* Python/Pise/__init__.pl: changed the remote parameter to
	location. 
	* Examples/python-examples/: change the remote parameter to
	location in some examples.

2003-05-16  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: removed test of zero file size to print the
	link. 

2003-05-13  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/squizz.xml: New program. A sequence/alignment format
	checker.

2003-05-09  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/hmmcalibrate.xml: seed flag bug fix.

2003-05-07  Nicolas Joly  <njoly@pasteur.fr>

	* Makefile.global (PROGRAMS): LASSAP interfaces are not installed
	anymore.

2003-05-06  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/mreps.xml: Updated for mreps v2.5.
	* Xml/consensus.xml: Pattern width fix.

2003-04-09  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/rnafold.xml: Avoid `rnafold.out' filename conflict
	(from program command line and batch stdout redirection).

2003-04-02  Nicolas Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl: Added some missing quotes around some
	`$command' strings.

2003-03-13  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Makefile: added blast_init.xml in distribution targets.

2003-03-12  Nicolas Joly  <njoly@pasteur.fr>

	* Makefile.global (PROGRAMS): do not install `most' program
	interface by default anymore.
	* Xml/stride.xml: pdbfile parameter type change to InFile (was
	Sequence).

2003-02-28  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/blast.xml: added blast_init.xml file

2003-02-28  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/fasta.xml: removed empty precond for alns parameter

2003-02-21  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/unroot.xml: removed terminal type hidden parameter: it
	was wrong (in retree, it is the graphics type parameter), and
	unuseful, since changing default produces a strange output.

2003-01-29  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/fasta.xml, Xml/fastapath.xml: made the path for Fasta
	databases path configurable.
	* README: comment about the fastapath.xml file
	* Makefile: added fastapath.xml in distributed files list.

2003-01-05  Catherine  Letondal  <letondal@pasteur.fr>

	* Scripts/statweb.pl: renewed script to compute statistics
	from bioweb log file

2002-12-11  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/quicktree.xml: a new program for NJ phylogeny.

2002-12-02  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/webmacro.pl: added lib/webmacro-bioperl-1.2.pl to use
	bioperl-run 1.2 Bio::Tools::Run Pise modules.

2002-12-02  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-html-utils.pl: added test for undefined email when
	piping. 

2002-11-29  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/sputnik.xml: new program interface, developped by Olivier
	Cantin from CBiB (olivier.cantin@pmtg.u-bordeaux2.fr)

2002-11-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: compute file size with an additional
	temporisation to cope with the disk latency problem (see file_size())

2002-11-25  Catherine  Letondal  <letondal@pasteur.fr>

	* Python/Pise/__init__.py: bug fix in PiseJob _submit() method when
	integer parameters; cosmetic cleaning in debug statements.

2002-11-20  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/Puzzle.xml: Simplify file input method.

2002-11-19  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/Puzzle.xml: Updated missing protein models for v5.0.

2002-11-18  Catherine  Letondal  <letondal@pasteur.fr>

	* Parser/PiseParser, Maker/perloo.pm, Maker/make-html-utils.pl, 
	* Maker/make-cgi.pl, lib/save.pl, lib/connect.pl, lib/help.pl, 
	* lib/results.pl, Makefile, Makefile.global: added support for
	optional email.

2002-11-14  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-html-utils.pl: added support for default local email
	(yielding no prompt in the Web interface)
	* lib/web.pl: added support for default local email

2002-11-12  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: added Squizz tests and warning message for
	sequence formats (locally).
	* lib/cancel_job.pl: Enables the user to ask for job cancellation
	when a problem occured with his/her sequence format.
	* Bio/Tools/Run/PiseJobParser.pm: added Squizz warning message
	handling
	* Bio/Tools/Run/AnalysisFactory/Pise.pm: changed email from
	mandatory to optional (changes in comments also)
	* Bio/Tools/Run/PiseApplication.pm: changed email from
	mandatory to optional.
	
2002-10-21  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/codonw.xml: Update for program version 1.4.2.

2002-10-18  Nicolas Joly  <njoly@pasteur.fr>

	* Makefile.global : Do not install `prodom' interface by default
	as it is out of sync with the databank.

2002-10-08  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Xml/fastasplitter.xml: splits a FASTA file into a set of smaller
	ones 

2002-10-07  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-realbioperl.pl: no prompt line when empty (else
	podchecker complains)
	* Bio: moved Bio::Factory::Pise to
	Bio::Tools::Run::AnalysisFactory::Pise and changed PiseApplication
	documentation accordingly.

2002-10-03  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/protpars.xml: quick and dirty bug fix for bootstrapping
	parameters 

2002-09-17  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: bug fix (bug introduced by change of
	2002-08-28 :-( ) 

2002-09-17  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/loadseq.xml: added trembl db

2002-09-12  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/mfold.xml: added *.ct files in available results

2002-09-05  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/wublast2.xml: Corrected output formats system, which wasn't
	working.

2002-08-28  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: added conversion of '<' and '>' characters in
	result file names to &lt; and &gt;

	* Xml/toppred.xml: changed some variable names in 2 words

2002-08-27  Catherine  Letondal  <letondal@pasteur.fr>

	* Makefile: added make-python target
	
	* Examples: sub-divided in 2 sub-directories for bioperl and
	python examples

2002-08-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-python.pl: a new generator for a Biopython client

2002-08-26  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/connect.pl: removed form based PISEDIR, VERSION,
	etc... variables initialization 

	* lib/initform.pl: same as lib/connect.pl
	
	* lib/results.pl: removed very old-fashioned CGI input read and
	form-based variables initialization

	* Maker/make-html.pl: simplified use and require statements
	(no PISEDIR and VERSION environment variables anymore)

	* Maker/make-html-utils.pl: same as Maker/make-html.pl
	
	* Maker/make-simple-html.pl: same as Maker/make-html.pl

	* Makefile: new light-distrib target, to build a smaller
	distribution file, containing only sources ; removed old
	PiseBioperl from all distributions
	
2002-08-25  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/results.pl: simplified web.pl require path

2002-08-22  Catherine  Letondal  <letondal@pasteur.fr>

	* Makefile: added phylip_header.xml and glimmer_header in the
	distribution list

2002-08-19  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/prot_nucml.xml: local Rearrangement search (-R)
	needs a mandatory Topology File.

2002-08-19  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw_convert.xml: bug fix in output files (thanks to
	Chris Ottolenghi) 
	* Xml/neighbor.xml: added seed parameter for multiple dataset +
	pipe for consense outtree

2002-07-18  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/pdbsearch.xml: new interface (pdbsearch program from
	C. Maufrais). 

2002-05-27  Catherine  Letondal  <letondal@pasteur.fr>

	* Examples: added toppred example

2002-05-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Bio/Factory/Pise.pm: bug fix in parameter init.

2002-05-21  Catherine  Letondal  <letondal@pasteur.fr>

	* Bio/ directory
	* Makefile: "real" bioperl distribution in Bioperl.tar.gz

2002-05-19  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-real-bioperl.pl: starting the final bioperl version (see
	Bio sub-directory) - included in PiseBioperl.tar.gz although previous
	system is still present (PiseBioperl subdirectory)

2002-05-16  Catherine  Letondal  <letondal@pasteur.fr>

	* Parser/PiseParser.pm: categories instead of category
	* Maker/make-sewer.pl: bug fixes, and added option -C
	* Xml/*.xml: added category in some programs definitions
	
2002-05-14  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-sewer.pl: bug fixes

2002-05-13  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/initform.pl: bug in default file generation ('"' characters
	not escaped) 

2002-05-13  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: added output files size to GCI results

2002-05-05  Catherine  Letondal  <letondal@pasteur.fr>

	* Parser/PiseParser.pm: added category field in PerlDef generated
	file
	* Maker/make-sewer.pl: generator for SeWer (see also SeWer
	sub-directory) 

2002-05-03  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-seqlab.pl: taken from Pise 2.d version and adapted to
	5.a. Not finished at all.

2002-04-25  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/dnapars.xml: jumble options must be provided when
	bootstrap. Messages changed and seqboott_seed used as jumble_seed
	when the latter is not provided.

2002-04-23  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/hmmbuild.xml: fixed output HMM file name filter (added a
	Results type)

2002-04-22  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/ACD: adaptation to EMBOSS 2.3.1

2002-04-18  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/smile.xml: new program (Structured Motif Inference and Evaluation)
	* Xml/smile2.xml: same with 2 boxes

2002-04-17  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/sreformat.xml: Hmmer 2.2g update.
	* Xml/alistat.xml, Xml/seqstat.xml, Xml/hmm*.xml: Likewise.

2002-04-16  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/fastdnaml.xml: added a Results parameter for temporary
	alignment files, that may contain useful information in case of
	error. 

2002-04-13  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: take an information message into account
	* lib/info.pl: where to set this information message
	* configure.in: added lib/info.pl

2002-04-12  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/bl2seq.xml: removed pipe for 2nd sequence

2002-04-11  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/webmacro.pl: upgraded to PiseBioperl new modules
	* PiseBioperl/PiseJob.pm: added methods to get hidden parameters
	values 
	* PiseBioperl/PiseJob.pm: added data structure to store hidden
	parameters values 

2002-04-10  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/rnaga.xml: New input formats (Stanford/Ig, Genbank, Nbrf and
	Embl).
	* Xml/dialign2.xml: EMBL sequence format supported by dialign2.

2002-03-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/blast2.xml: paragraph for html4blast options
	* Parser/PiseParser.pm: expansion of paragraph precond to all
	included parameters

2002-03-22  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/boxshade.xml: PICT output file named boxshade.pict instead
	of boxshade.result
	* Xml/melting.xml: added reference.

2002-03-08  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/fasta.xml: Option `-k' does not exist anymore in
	fasta34t10d3.

2002-03-07  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/protdist.xml: Added Weight options
	* Xml/dnadist.xml: Added Weight options

2002-03-07  Katja  Schuerer  <schuerer@pasteur.fr>

	* Xml/dnapars.xml: Added Weight options + pipe for weights file

2002-03-07  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/phiblast.xml: Updated html output mecanism.

2002-02-27  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/CSR.xml: references corrected; pdb output piping added.

2002-02-15  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/neighbor.xml, Xml/protdist.xml, Xml/fitch.xml: Phylip 3.6a2
	update.

2002-02-14  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/protpars.xml: Phylip 3.6a2 update.
	* Xml/dnapars.xml: Phylip 3.6a2 update.
	* Xml/dnadist.xml: Phylip 3.6a2 update.
	* Xml/seqboot.xml: Phylip 3.6a2 update.

2002-02-11  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/drawgram.xml: Phylip 3.6a2 update.

2002-02-09  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/mreps.xml: New program.

2002-02-08  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/mix.xml, Xml/clique.xml, Xml/consense.xml, Xml/kitsch.xml:
	Phylip 3.6a2 update.

2002-02-07  Nicolas Joly  <njoly@pasteur.fr>

	* Xml/drawtree.xml: Phylip 3.6a2 update.

2002-02-06  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: variable result_remain initialized from a
	global configuration variable $RESULT_REMAIN in lib/web.pl)
	* lib/web.pl: default for $RESULT_REMAIN is 10 (instead of 5)

2002-01-25  Catherine  Letondal  <letondal@pasteur.fr>

	* PiseBioperl/PiseJob.pm: added a lookup_piped_file to search for
	a pipe typed result.

2002-01-17  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/dca.xml: Input format is FASTA.

2002-01-16  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Xml/consensus.xml: some option flags documentation added

2002-01-08  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/prot_numl.xml: phylip_dist pipe on molphy.results when mode -D

2002-01-07  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/njdist.xml: output files (tree and topology)

2001-12-11  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/unroot.xml: comment on tree format.
	* Xml/dca.xml: added references.

2001-12-08  Catherine  Letondal  <letondal@pasteur.fr>

	* PiseBioperl/PiseJob.pm: bug fix in READLINE (skip of empty lines)

2001-12-01  Catherine  Letondal  <letondal@pasteur.fr>

        * Xml/unroot.xml: use of RETREE Phylip program to unroot a tree
        * Makefile.global: added unroot in the PROGRAMS list

2001-11-29  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/results.pl: bug in PISEDIR path

2001-11-26  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-bioperl.pl: new interface generator for bioperl
	* PiseBioperl: classes for a Pise/bioperl API. Contains example 
	scripts.
	* Makefile: targets for bioperl API generator
	* Xml/dnapars.xml: outgroup ctrl
	* Xml/neighbor.xml: outgroup ctrl
	* Xml/clustalw.xml: profile and sequence actions data files

2001-11-21  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw.xml: help and prompt for -outputtree parameter

2001-11-18  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/check_user.pl: use of REMOTE_ADDR instead of REMOTE_HOST
        if latter not defined

2001-11-14  Catherine  Letondal  <letondal@pasteur.fr>

	* Makefile: distrib target

	* Maker/make-html-utils.pl: if defined, default value inserted in
	[default] part of an Excl parameter (instead of "")

	* Xml/toppred.xml: changes in paragraphs

2001-11-14  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: discards index.html file from files list
	displayed in results page.

2001-11-13  Nicolas  Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl:  Allow extra leading/trailing spaces in
	fetched sequences from database entries.

2001-11-06  Nicolas  Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl: Check for PBS qsub command status and panic
	on failure.

2001-10-26  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Xml/prose.xml: Added author.
	* Maker/make-cgi.pl: Test if too many (> 10) files to send by email.

2001-10-17  Nicolas  Joly  <njoly@pasteur.fr>

	* lib/pbs.pl: New file, for PBS specific functions.
	* Maker/make-cgi.pl: Use it.
	
2001-10-10  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/dnadist.xml: Add check to avoid program loop.

2001-09-24  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/wise2.xml: Updated for wise2 v2.1.22c.
	* Xml/weighbor.xml: Updated for weighbor v1.2.

2001-09-14  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Maker/make-cgi.pl: fix in tmp dir name for piped files to adapt
	to PBS directory file names

2001-09-13  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Maker/make-cgi.pl: changed displayed address in case of panic to
	HELP. 

2001-09-13  Katja  Schuerer  <schuerer@electre.pasteur.fr>

	* Xml/trnascan.xml: update to tRNAscan-SE version 1.21 - add
	options -A, -G(old -G -> -O), -H, -B

2001-09-12  Katja  Schuerer  <schuerer@electre.pasteur.fr>

	* Xml/fasta.xml: update to version 34 - add options -B, -F, -i,
	-j, -r, -S, -x

2001-09-12  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Parser/PiseParser.pm: concatenation for prompt attribute in
	procedure characters (instead of mere assignation), since XML
	entities such as &lt; are feeded separately to this procedure.

2001-09-10  Katja  Schuerer  <schuerer@electre.pasteur.fr>

	* Xml/prose.xml: add new interface for prose (Prosite pattern
	search in protein sequences)
	* Xml/psiblast.xml: add interface for PSI-BLAST former integrated
	in BLAST2 
	* Xml/blast2.xml: PSI-BLAST no longer integrated, add tabular
	output format
	* Xml/bl2seq.xml: update to blast version 2.2, add flags '-I',
	'-J' and tabular output format
	
2001-09-10  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Maker/make-html-utils.pl: default value for Excl not taken into
	account when 0

2001-09-07  Nicolas  Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl: Check for no more than one batch system at
	one time.

2001-09-06  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/html4blast.xml: New `-l' and `-q' flags.
	* Xml/golden.xml: Added `prosite' database.

	* Maker/make-cgi.pl: New support for PBS (Portable Batch System).
	* lib/wrapper.pl: New file, PBS helper script.
	* lib/web.pl: New `$PBS' variable.

2001-09-06  Eric  Deveaud  <edeveaud@pasteur.fr>

	* Xml/mview_blast.xml: Added -alignment flag.
	* Xml/mview_alig.xml: Likewise.

	* Xml/mspcrunch.xml: Corrected -X flag,
	added -j, -A, -N and -O flags.
	
	* Xml/molphy.xml: No longer exists, it is splitted in
	prot_nucml.xml and njdist.xml.

	* Xml/prot_nucml.xml: New interface, for protml and nucml
	added (in regard to molphy interface).
	-m, -mf, -R, -RX,  -p #, -M and -S flags.

	* Xml/njdist.xml: New interface, njdist added (in regard to molphy
	interface).  -U, -S and -t str flags.
	
	* Xml/melting.xml: Added parameters for dangling ends and
	mismatches
	
	* Xml/extractcds.xml: Corrrected -p flag Show product in
	description.

	* Xml/toppred.xml: Modified interface to feet with the new
	toppred implementation.

2001-09-04  Catherine  Letondal  <letondal@electre.pasteur.fr>

	* Maker/make-html-utils.pl: mandatory icon for Excl type paramter
	if no vdef defined.

2001-09-03  Nicolas  Joly  <njoly@pasteur.fr>

	* Maker/make-cgi.pl: Rename `$batch_command' to `$lsf_command' for
	future PBS batch system support.

	* lib/batch.pl: New file, for batch queues selection.

	* lib/*.pl: use perl `localtime' instead of `date` calls.
	Likewise for `basename`.

	* lib/check_user.pl (not_wanted): New check for Pasteur local
	users.

	* Makefile (rxp): Removed obsolete `-e' flag.

Tue Aug 21 10:30:26 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw.xml: added *.phb mask in phylipnewtreefile
	parameter 

Fri Jul 27 16:22:51 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: change in test for batch command
	if ($LSF) and not if ($PASTEUR || $LSF)

Mon Jul 23 19:06:35 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: bug fix in print statement

Mon Jul  2 20:15:44 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/prosearch.xml: updated title, description, authors and added
	reference.

Mon Jun 18 09:49:07 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-biok.pl: small bug fixes

Fri Jun 15 11:53:07 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw.xml: Phylip output format gave a bug in the
	pipetype recognition.

Thu Jun 14 18:35:40 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-biok.pl: simple/advanced level
	* lib/biok.pl: simple/advanced level

Wed May 30 09:28:12 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/consensus.xml: added a control on the protein/dna choices

Fri May 25 19:01:10 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/boxshade.xml: parameter sequence_characters restricted to
	254 (maximum allowed by boxshade - not documented) + *.result for
	PICT format

Mon May 21 15:29:44 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-biok.pl changed (data/view separation).

2001-05-21  Nicolas  Joly  <njoly@pasteur.fr>

	* Parser/pise.dtd: Added optional program version.

Fri Mar 30 16:42:25 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* EMBOSS: files for version 1.11.0

Wed Mar 28 17:51:17 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-cgi.pl: added documentation links and references in
	the CGI results pages

Tue Mar 13 13:28:38 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/psort2.xml: HTML output enabled (-w)

Tue Mar  6 09:12:03 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* configure: MIME::Lite made mandatory.

Mon Mar  5 19:00:23 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/web.pl: variable DONT_EMAIL_RESULTS: if set to 1, results
	are never sent by email (notification by url only)
	* Maker/make-cgi.pl: variable DONT_EMAIL_RESULTS: don't display the
	results delivery choice menu, set the default result type to url.

Wed Feb 14 11:51:59 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Makefile.global: added recode, abiview and coderet.

Thu Feb  8 09:49:06 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw.xml: tree output files with .phb suffix are now
	seen as Phylip trees.

Thu Feb  1 18:15:32 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* EMBOSS: files for version 1.9.1.
	* Maker/ACD/parser.y
	* Maker/ACD/do_xml.pl:	the ACD parser recognizes the entry
	attribute for sequences; when true, no fasta conversion will be
	performed. 

2001-02-01  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/protdbs.xml: Remove Genpept GSS section which has no
	sequences. Reconstruct needed interfaces.

2001-01-29  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/melting.xml: Added concentrations limits.

2001-01-29  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/toppred.xml: added sequence format specification: raw (13)

Wed Jan 24 17:01:09 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/toppred.xml: added a new program (TopPred 2: Topology
	prediction of membrane proteins (Heijne, Wallin, Claros).

2001-01-15  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/golden.xml: Added `sptrnrdb' database.

Mon Jan 10 12:00:00 2001  Frederique  Galisson  <galisson@pasteur.fr>

	* Xml/blast2.xml: created a new paragraph for "filtering and
	masking options", taking into acount some of the new
	filtering/masking features of the last NCBI-blast2 versions.

	* Xml/wublast2.xml: replaces the old "blastwu" interface (major
	changes, taking into account the news parameters proposed in the
	licensed version of WU-Blast2).

	* Xml/dca.xml: switched the -a option to on as a default (for the
	running time is too long with the exact cut positions, and that
	what is done on the DCA server at Bielefeld )

Mon Jan  8 10:27:43 2001  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/golden.xml: added a new program (a fast database entries
	fetching program by N. Joly)

Fri Dec 29 16:25:22 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/save.pl: action= ... configured with
	CGI_URL instead of CGI_DIR
	* lib/webmacro.pl: $MACROS_DIR = "$ROOT_WEB/$CGI_DIR/macros
	changed to $MACROS_DIR = "$CGI_DIR/macros";
	* Maker/make-biok.pl: another generator (in construction)
	* Makefile: statements for this generator

Wed Dec 27 11:23:03 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* Xml/clustalw.xml: added precond for infile - if actions =
	-profile, infile is not mandatory
	* Maker/make-cgi.pl: action= ... connect.pl configured with
	CGI_URL instead of CGI_DIR

Mon Dec 18 00:08:06 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* lib/webmacro.pl: a missing @PERL@ for perl path

Wed Dec 13 17:50:22 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-connections.pl: added a print 1; at the
	end of the generated PerlDef/pipeins

Tue Dec 12 14:13:27 2000  Bernard  Caudron  <caudron@pasteur.fr>

	* Xml/codonw.xml: Correct misspelled option -gc3s

Mon Dec  4 10:34:58 2000  Nicolas  Joly  <njoly@pasteur.fr>

	* Xml/saps.xml: Fixed input format value by removing `-b' flag.

Fri Dec  1 11:44:27 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* Maker/make-html-utils.pl: fixed SIZE= according to default value in 

Wed Nov 29 11:24:15 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* Phylip files: Added control for outgroup parameter.
	XML files only distribution (Pise-xml.tar.gz).
	Removed HOME definition from emboss.xml
	New programs:
		PIMA

Wed Nov 22 11:24:15 2000  Catherine  Letondal  <letondal@pasteur.fr>

	* Start of file ChangeLog (ok... it's never too late).
	Fixed H1 blocks in HEAD blocks.
	XML parameter in blast2 (-m 7).
