X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FwebServices%2FJABAWS.html;h=6750b55a69cb3827da8204c64c4a236819b02456;hb=86169de3e5687709d1635a14cefea406517f19c8;hp=90de537816515a7618265fbe24ad9c8072f184a1;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html index 90de537..6750b55 100644 --- a/help/html/webServices/JABAWS.html +++ b/help/html/webServices/JABAWS.html @@ -1,78 +1,81 @@ + - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . ---> - + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> The JABAWS system -

The JAva Bioinformatics -Analysis Web Services -system (JABAWS)
-Jalview includes a client for interacting with programmatic (SOAP) web -services for the JABAWS -service model, developed at the University of Dundee by Peter Troshin -and Geoff Barton. This is an open source system that provides a -framework for wrapping command line bioinformatics analysis programs -that enables them to be executed locally or on a cluster using data and -analysis parameters provided by a program linked with JABAWS directly or -accessing it remotely via its web services interface.

-

The list of JABAWS servers known to the Jalview desktop is shown -in the Web Services Preferences -Panel, and detailed information about a particular service is available -from the help text and web pages accessible from its job parameters dialog box.

-

Obtaining JABAWS
-One of the aims of JABAWS is to enable you to easily perform -computationally intensive bioinformatics analysis tasks using your own -computational facilities. It can be installed on a workstation to -provide stand-alone execution of analysis programs, or as a job -submission engine - enabling larger numbers of jobs to be handled. If -you would like to download and install JABAWS for your own use, please -go to http://www.compbio.dundee.ac.uk/jabaws -for more information.

-

Configuring your own JABAWS services for use by -Jalview
-Once you have downloaded and installed JABAWS, and verified it is -working, all that is needed is to add your new JABAWS server's URL to -the list in the Web Services -Preferences Panel. After adding your service and saving your preferences -or hitting the 'refresh web services' button, you should be able to -submit jobs to the server via the alignment window's web services menu. -Your JABAWS servers list is stored in your Jalview preferences, so you -will only have to configure Jalview once for each new server.

-

Support for accessing JABAWS servers was introduced in -Jalview 2.6.

+

+ The JAva Bioinformatics + Analysis Web Services + system (JABAWS)
Jalview + includes a client for interacting with programmatic (SOAP) web + services for the JABAWS + service model, developed at the University of Dundee by Peter + Troshin and Geoff Barton. This is an open source system that + provides a framework for wrapping command line bioinformatics + analysis programs that enables them to be executed locally or on a + cluster using data and analysis parameters provided by a program + linked with the JABA engine directly or accessing it remotely via + its web services interface. +

+

+ The list of JABAWS servers known to the Jalview desktop is shown in + the Web Services Preferences + Panel, and detailed information about a particular service is + available from the help text and web pages accessible from its job parameters dialog box. +

+

+ Obtaining JABAWS
One of the aims of JABAWS + is to enable you to easily perform computationally intensive + bioinformatics analysis tasks using your own computational + facilities. It can be installed on a workstation to provide + stand-alone execution of analysis programs, or as a job submission + engine - enabling larger numbers of jobs to be handled. If you would + like to download and install JABAWS for your own use, please go to http://www.compbio.dundee.ac.uk/jabaws for more information. +

+

+ Configuring your own JABAWS services for use by + Jalview
Once you have downloaded and installed JABAWS, + and verified it is working, all that is needed is to add the URL for + your JABAWS server(s) to the list in the Web Services Preferences Panel. After adding your service and + saving your preferences or hitting the 'refresh web services' + button, you should be able to submit jobs to the server via the + alignment window's web services menu. Your JABAWS servers list is + stored in your Jalview preferences, so you will only have to + configure Jalview once for each new server. +

+

+ Support for accessing JABAWS servers was introduced in + Jalview 2.6. +

+

+ Option for adding JABAWS servers which fails validation was + introduced from version 2.8.2 +