Basel, May 22, 1994
The Swiss Node of the European Molecular Biology Network (EMBnet) is
pleased to announce the availability of the Hierarchical Access System for
Sequence Libraries in Europe, HASSLE, release 4.1.
HASSLE currently runs on many EMBnet hosts and covers features like FASTA and
BLAST searching, PROFILESEARCH and MOWSE searching, and other tools of biolo-
gical interest. This post is meant to address system administrators who are
interested to run own services, or end users who would like to make their
administrators interested.
Both Provider and Customer software are available in full source and are ex-
tensively documented (postscript; about 120 pages, dvi or full LATEX source
alternatively). The software was originally developed on the IRIX operating
system (Silicon Graphics) but to maintain optimal conditions at our site we
switched to the OSF/1 operating system (Digital Equipment). Starting from the
base code, we made it run by adding modifications for the various UNIX fla-
vours and on the VMS operating system (Digital Equipment) for the VMS sites.
A AXP/VMS system running UCX TCP/IP services was used for the original setup,
but other emulations are supported as well.
The following operating systems have been verified to run HASSLE:
VMS System Customer Provider UNIX System Customer Provider
VMS 5.4 UCX 1.3 X IRIX 4.0x X X
VMS 5.4 UCX 2.0 X IRIX 5.0x X X
VMS 5.5 UCX 2.0 X X Sun OS 4.x X X
VMS 5.4 Multinet 3.0 X X Ultrix 4.x RISC X X
VMS 5.5 TCPWare 3.1 X Ultrix 4.x VAX X
VMS 5.5 Multinet 3.2 X X OSF/1 X X
AXP 1.0 Multinet 3.2 X X Convex 10.1 X
AXP 1.5 UCX 3.0 X X HP/UX X
AXP 1.5 Multinet 3.2 X X LINUX X
AXP 1.5 TCPWare 3.2 X X Solaris 2.3 X X
IBM AIX X X
Most of the currently available tools focus on the integration into the
software environment of the Genetics Computer Group Package (Version
7 currently,Version 8 coming later this year) (GCG Inc, Madison, Wisconsin)
Other tools feature general sequence retrieval or make use of other soft-
ware, such as the MOWSE server in the UK (UK EMBnet node) or the dedicated
hardware BIOCELLERATOR (compugen Ltd, Rehovot) (Israelian EMBnet node).
The software is available free of charge from bioftp.unibas.ch or, pre-
ferably, from the mirror nic.switch.ch (in the mirror/embnet-ch directory).
You are encouraged to develop own TOOLS to raise the functionality. We
will demo the software on this year's business meeting of EMBnet,associated
to the 3rd international GPC conference in Chester. HASSLE was described in
the January issue of CABIOS.
"NOTE.ME" file follows
i
***********************************************************
* *
* H A S S L E *
Hierarchical Access System for Sequence Libraries in Europe
* *
***********************************************************
V E R S I O N 4 . x , 1 9 9 4
===========================================================================
The HASSLE protocol and its associated software modules Customer, Master,
Responder, and the local processing programs ( used collectively with the
name HASSLE in the following text) in its current Version 4 are copyrighted
by Biocomputing Basel, and available freely without cost.
The distribution of the software shall strictly follow the following rules:
o HASSLE may not be sold, as a whole or in pieces. HASSLE code may be
used, adopted, incorporated in any program package, commercial, share-
ware or public domain, as long as the provider of this program package
makes sure that (a) the HASSLE layer is always up to date with the cur-
rent HASSLE release version and (b) the incorporation is performed in a
fashion that allows to access the source code, or use HASSLE as provi-
ded by the original distributor Biocomputing Basel.
o HASSLE may not be used in a commercial environment in order to generate
profit from services which are accessing the services available via the
HASSLE protocol.
o HASSLE may be adopted by any service provider, commercial, non-profit,
academic, or any other, in the understanding that the provider offers
services to the community without charge within the limits of reasona-
bility. Exceeded limits may not be used as argument to charge for the
service (see above).
o HASSLE source code is available for the current version 4. In order to
keep the communication layer free of trouble, any deviation from the
protocol specifications (on port 375) is prohibited. Source code fixes,
changes, enhancements etc. are most welcome if documented and communi-
cated to the authors. After evaluation, the changes will possibly be
considered in a new full release version or immediately released as in-
cremental version if a bug fix is required.
o HASSLE may be placed on any file server, as long as it is made sure that
the distribution and documentation are kept up-to-date.
o HASSLE customers and providers should always send the registration as
distributed with the package in order to be informed and kept up-to-
date with the development and announcements.
===========================================================================
***********************************************************
* *
* H A S S L E *
Hierarchical Access System for Sequence Libraries in Europe
* *
* *
* This program package has been written starting from '92 *
* at the Biocomputing Laboratory, University of Basel, by *
* Reinhard Doelz. Valuable suggestions from various col- *
* leagues, including code contributions (as documented), *
* allowed to make this code portable, and running on the *
* different platforms. Though it has been a major effort *
* to make the HASSLE protocol suite and its tools work, *
* no responsibility can be taken for errors which *
* might occur while running or result from processing the *
* program's output. The program writing was supported by *
* Basel University, and a grant from the Swiss National *
* Science Foundation (NF). The software resembling HASSLE *
* may be copied and resdistributed only if this statement *
* is preserved. HASSLE may not, as a whole or in part, *
* sold or used by commercial institutions to gain profit *
* from the services accessed on the basis of academic re- *
* search. Users should acknowledge the program package *
* (Doelz, R., Hierarchical Access System for Sequence *
* Libraries in Europe (HASSLE): a tool to access sequence *
* databases remotely. Comput-Appl-Biosci. 10(1), 31-35, *
* 1994) if results to be published are obtained. All *
* software accessed with the system is copyrighted sepa- *
* rately by corresponding vendors and need to be cited in *
* publications. *
***********************************************************
+---------------------------+-------------------------------------------+
| Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 |
| Biocomputing | electronic Mail doelz at urz.unibas.ch |
|Biozentrum der Universitaet+-------------------------------------------+
| Klingelbergstrasse 70 | EMBnet embnet at comp.bioz.unibas.ch |
|CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch |
+---------------------------+------------- http://beta.embnet.unibas.ch/
Thanks:
To Ute, Juergen and Marianne for the patience; for the funding contribu-
tions from Basel University, Schweizer Nationalfonds, Silicon Graphics
and Digital Equipment; and various suggestions, contributions, and code
fragments from (alphabetically) K.Adelmann, R.Appel, F.Eggenberger,M.Egger,
J.Epstein,T.Etzold,the whole GCG Team,D.Gilbert,A.Godknecht,M.Hage,R.Harper,
P.Linder,R.Lopez,H.Moeller,R.Omond,F.Roesel,L.Rosenthaler,P.Stoehr,P.Zimak.
$Id: NOTE.ME,v 1.3 94/02/27 19:04:20 doelz B4-1-0 $
Special thanks for version 4.1 go to
Jeroen Coppieters, University of Gent (HASSLE AIX)
Martin Kroeker, TH Darmstadt (HASSLE AIX, ascomp bug)
Giompieno Marcenano, University of Genua (HASSLE HP/UX)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
This is HASSLE 4.1 full release (D4-1-0) and for internal
and external use. The fortran-written tools are NOT updated.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
CHANGES TO HASSLE 4.0:
fixed/changed:
--------------
table size problem indicating faulty table member in nslookup
changed names in uppercase to avoid double table population
customer does no longer die upon rejected transmission
customer does no longer die if local file not found in responder mode
customer does no longer die upon wait time expiration
customer does report on routine in upper layers rather than exit silently
removed:
--------
DUMB compilation directive (was unsupported anyway)
WAITFOR statement for other than CUSTOMER
added:
------
-o (/only_dumb) flag
-n (/nodumb) for MASters to reject , can be enforced as default by
specifying -DNODUMB
-l (/local) for local configuration file
-z 504 for report on commandline flags
add WAITFOR implementation in client.c
add SWITCH recognition in client.c
add WAITFOR recognition in asyn.c
add DUMB to SERVICE file (in hassle.com/hassle.csh recognition)
allowed client module to read absolute pathnames
added local configuration file capability
added INSTANT HASSLE as binary distribution; this one can't do servers
AIX and LINUX, as well as SOLARIS, now run fine
to be done:
-----------
API documentation in detail
documentation update
tools update (must wait for GCG 8)
HP/UX
cleanup of code and detailed exit status
update service (transmission of binaries)
and a lot of others
ADDED AFTER BETA 4.1
-=-=-=-=-=-=-=-=-=-=-=
removed bug in ascomp (thanks Martin Kroeker)
added HP/UX
DISCLAIMER
Note that the software mentioned resembles Computer Program(s) which
require a license in order to be run unless stated otherwise in a state-
ment codistributed with the software. The use of the program(s) was men-
tioned within a specific problem or example and must not be used to con-
clude that other software products cannot possibly do a similar job.
--
+----------------------------------+-------------------------------------+
| EMBnet SWITZERLAND | RFC embnet at comp.bioz.unibas.ch |
| Biocomputing | (small) FTP and GOPHER server |
