From be0f89ace46c43245372ed67894d034eab71f281 Mon Sep 17 00:00:00 2001 From: Sasha Date: Fri, 28 Jun 2013 14:55:40 +0100 Subject: [PATCH] Update manual and other static html page for JABAWS 2.0.1 --- website/contacts.html | 29 +++---- website/develhome.html | 15 ++-- website/index.html | 142 ++++++++++++++++++-------------- website/man_about.html | 175 +++++++++++++++++++++++----------------- website/man_awscloud.html | 89 ++++++++++---------- website/man_awscloud_bs.html | 91 ++++++++++----------- website/man_awscloud_ec2.html | 77 +++++++++--------- website/man_client.html | 76 ++++++++--------- website/man_configuration.html | 81 +++++++++---------- website/man_dev.html | 80 +++++++++--------- website/man_server_dev.html | 66 +++++++-------- website/man_servervm.html | 108 ++++++++++++------------- website/man_serverwar.html | 87 ++++++++++---------- website/man_stats.html | 67 ++++++++------- website/manual_qs_amazon.html | 93 +++++++++++++++++++++ website/manual_qs_client.html | 90 ++++++++++----------- website/manual_qs_va.html | 71 ++++++++-------- website/manual_qs_war.html | 68 ++++++++-------- website/quick_start.html | 56 ++++++------- 19 files changed, 826 insertions(+), 735 deletions(-) create mode 100644 website/manual_qs_amazon.html diff --git a/website/contacts.html b/website/contacts.html index dbc9ae1..778285f 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -4,26 +4,25 @@ - -Java Bioinformatics Analysis Web Services (JABAWS) download -page + +Java Bioinformatics Analysis Web Services (JABAWS) download page - + +
- +
Home Getting Started @@ -52,12 +51,10 @@ page
- + +
-
+Java Bioinformatics Analyses Web Services (JABAWS) main page + + + + +
+ - +
-

JABAWS 2.1

-

JABAWS is free software which provides web services for multiple sequence alignment, prediction of protein disorder, and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.1 introduces protein disorder prediction services based on DisEMBL, IUPred, Ronn, GlobPlot and protein sequence alignment conservation measures calculated by AACon. A new multiple sequence alignment service for Clustal Omega is also provided, in addition to standard JABAWS:MSA services for Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. -JABA Web Services can be accessed from the Jalview desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.
+

JABAWS 2.0.1

+

JABAWS +is free software which provides web services for multiple sequence alignment +(programs available: Clustal Omega, Clustal W, +MAFFT, MUSCLE, +, TCOFFEE and PROBCONS), +prediction of protein disorder (programs available: DisEMBL, IUPred, +Ronn, GlobPlot), +and amino acid conservation (program available: AACon) +conveniently packaged to run on your local computer, server or cluster. + +JABA Web Services can be accessed from the Jalview desktop application and provide multiple alignment +and sequence analysis calculations limited only by your own local computing resources.

-Please note that JABAWS 2.1 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012). In the meantime you can access all JABAWS2.1 services through the JABAWS command-line client.

+Please note that JABAWS 2.0.1 is supported by Jalview 2.8 onwards. You can also access all JABAWS 2.0.1 services through the JABAWS command-line client.

+

For System Administrators

+
+

The Server: JABAWS Web Application aRchive (55M)

+

JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. + Please check the quick start guide for installation instructions.

+
+ - + + +
-
+

For Users

- The Server: JABAWS Virtual Appliance: (520M) - or use JABAWS on Amazon Webservices Cloud
- The Client: Jalview (18M) -

To use JABA Web Services on most operating systems, just download and install the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!

+ The Server: JABAWS Virtual Appliance: (440M) + or JABAWS on Amazon Webservices Cloud
+ The Main Client: Jalview (18M) +

To use JABA Web Services on most operating systems, just download and install + the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!
-

For System Administrators

-
-

The Server: JABAWS Web Application aRchive (55M)

-

JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for installation instructions.

-
-
-

For Bioinformaticians/Developers

-
+

For Bioinformaticians/Developers

+
The Server: JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source - - - -

You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public server (see below) with the command line client or you own script. + Command Line Client binary | source + +

+You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. +The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public +server (see below) with the command line client or you own script. Check out the quick start guide for further details.

-
-

Public JABAWS Server

-

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. The latest versions of Jalview are configured to use public JABAWS server by default.

+

You can access our public JABA Web Services with our command line client, + Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.0.1. + The latest versions of Jalview are configured to use public JABAWS server by default.

  • The JABAWS public web services address is http://www.compbio.dundee.ac.uk/jabaws
  • A detailed web services description is available from here: WSDL List
-

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

+

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, + or if you are concerned about privacy or on an unreliable network connection, then you can + download and run the JABAWS Server on your own hardware.

Previous versions of JABAWS

-

JABAWS 1 is available from here http://www.compbio.dundee.ac.uk/jabaws1. We advise you to update to the JABAWS 2 as this version is fully backward compatible with JABAWS 1 and contain numerous improvements. Please consult the manual for more information on versions compatibility.

+

Old JABAWS version is available here: + http://www.compbio.dundee.ac.uk/jabaws1 and + http://www.compbio.dundee.ac.uk/jabaws2. + We advise you to update to the JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and + contain numerous improvements. Please consult the manual for more information + on versions compatibility. +

Reference

-

Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.

+

+ Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for +Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics 2011; + +doi: 10.1093/bioinformatics/btr304.

-
+ + +
+ - + + +
+ -
+ +

JABAWS MANUAL

About

@@ -59,19 +64,30 @@
  • Programmatic access to JABAWS
    • -

    What is JABAWS?

    -

    JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of currently supported programs) from Jalview. - Future versions of JABAWS will incorporate many other tools.

    +

    + JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a + collection of web services for bioinformatics, and currently provides services that make it easy + to access well-known multiple sequence alignment and protein disorder prediction programs + (see the list of currently supported programs) from Jalview. + Future versions of JABAWS will incorporate many other tools. +

    Getting JABAWS

    -

    JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need.

    +

    + JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and + run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS + Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your + lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure + but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested + in writing your own client, the JABAWS command line client is what you need.

    JABAWS Benefits

    • Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
    • Comes complete with sources and binaries for all the bioinformatics programs that it runs.
    • Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
    • Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
      • -
    • Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, your lab's server, or the publicly available services at the University of Dundee.
      • +
    • Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, + your lab's server, or the publicly available services at the University of Dundee.
    • Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.
    • Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.
    @@ -98,52 +114,62 @@ -

    What is new in JABAWS 2?

    -

    Comparing to previous version of JABAWS JABAWS 2 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains

    -
    • updates for all multiple sequence alignment services
      • +

      What is new in JABAWS 2.0.1?

      +

      Comparing to previous version of JABAWS 2.0.1 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains

      +
      • updates for all multiple sequence alignment services
      • four new protein disorder prediction services
        • -
      • Clustal Omega multiple sequence alignment web service
        • -
      • amino acid conservation service
        • +
      • Clustal Omega multiple sequence alignment web service
        • +
      • amino acid conservation service
      • web services execution statistics visialization
        • -
      • web services status check from a web page
        • +
      • web services status check from a web page
      • VirtualBox support was dropped in favour of VMware
        • -
      • new WAR package for Mac users
        • -
      • Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
        • -
      • Improved web services client API
        • -
      • Simplified WAR package installation
        • +
      • new WAR package for Mac users
        • +
      • Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
        • +
      • Improved web services client API
        • +
      • Simplified WAR package installation
      - -

      What is JABAWS client?

      - -

      A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. -The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods -on any instance of JABAWS Server that it can reach over the web. It is useful if you -want to test, or execute the programs provided by a JABAWS server in your own scripts, and do not want to handle any web service -specific details. The client is open source, so you can also use its source code to find -out how to work with JABA Web Services if you would like to write your own client -software. Jalview, which is a multiple sequence alignment and analysis application, provides a graphical JABAWS client. This client has the same -functionality as the command line client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

      + +

      What is JABAWS client?

      + +

      + A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web + services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web + services methods on any instance of JABAWS Server that it can reach over the web. It is useful if you want to + test, or execute the programs provided by a JABAWS server in your own scripts, and do not want to handle any web + service specific details. The client is open source, so you can also use its source code to find out how to work + with JABA Web Services if you would like to write your own client software. + Jalview, which is a multiple sequence alignment and analysis application, + provides a graphical JABAWS client. This client has the same functionality as the command line client, but + instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. +

      JABAWS versions compatibility and Jalview support

      -

      JABAWS version 2 is fully backward compatible with JABAWS version 1. That means that all JABAWS 1 clients should be able to use JABAWS 2 instead. However, they will be limited to the multiple sequence alignment web services only. To benefit of new web services introduced in JABAWS 2 the clients have to be updated.
      -Jalview since version 2.6.1 integrates fully with JABAWS 1. Therefore it will be possible to use any versions of Jalview after 2.6.1 with JABAWS 1. However, the full support for JABAWS 2 is introduced in Jalview version 2.8 or later.

      +

      + JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and + v2.0 clients should be able to use JABAWS 2.0.1 instead. To benefit of new web services introduced in JABAWS 2.0 + the clients compitible with JABAWS v1.0 have to be updated. +

      Programmatic access to JABAWS

      -

      JABA Web Services are WS-I basic profile compliant, which means they can be accessed using -any programming language or system that can utilize standard SOAP web services. -The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate -service bindings for your program. If you use Java, however, then you may wish to use our -client package to access JABAWS. -This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings; -but in addition, offers some additional methods which simplify working with JABAWS. For more information please refer to the -data model javadoc. +

      +JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language +or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home +page, and you can use this to automatically generate service bindings for your program. If you use Java, however, +then you may wish to use our client package to access JABAWS. +This package is based on the autogenerated source code produced by wsimport, which +is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify +working with JABAWS. For more information please refer to the data model javadoc.

    - + +
    -
    + + +
    + - diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 8bef1f4..2ec115c 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -3,58 +3,58 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - -Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual - - + +Java Bioinformatics Analyses Web Services (JABAWS) Server Amazon Cloud Manual + + +
    +
    + +
    - + +

    JABAWS MANUAL

    JABAWS Server in the Amazon Cloud

    JABAWS on the Cloud

    @@ -66,18 +66,11 @@

    If you know what to do than JABAWS AMI ID is ami-d1d5e9a5, manifest 846107356395/JABAWS 2 to get you started, if not please refer to How to use JABAWS on the Amazon EC2 cloud pages.

    Alternatively you can use JABAWS on the Amazon Elastic BeanStalk. You may want to use this option to deploy JABAWS in the cluster configuration.

    -
    - -
    - - -
    - - - - + + + + + - + +
    +
    + +
    - + +

    JABAWS MANUAL

    -

    How to use JABAWS on Amazon Elastic Beanstalk

    +

    How to use JABAWS on Amazon Elastic Beanstalk

    1. Create Amazon Web Services account.
      2. @@ -66,23 +63,17 @@
    2. Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS.
      3. Elastic Beanstalk launch JABAWS war step 3 -
    3. Choose the type of hardware you want to run JABAWS on.
      4. +
    4. Choose the type of hardware you want to run JABAWS on.
      5. Elastic Beanstalk launch JABAWS war step 4
    5. If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com
      6. Elastic Beanstalk launch JABAWS war

     

    -
    -
    - - -
    - - - - + + + + + - + +
    +
    +
    - + +

    JABAWS MANUAL

    How to use JABAWS on the Amazon EC2 cloud

      -
    1. Create Amazon Web Services account.
      2. +
    2. Create Amazon Web Services account.
    3. Log in into the Amazon Web Services (AWS) console. Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1.
    4. Click on "Launch Instance" button marker 2.
      5. @@ -77,7 +73,6 @@
    5. Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance SSH is not necessary, you can do this from the Amazon Webservices Console (AWS).
      6. - ese
    6. Review the configuration and launch the instance, then click "view your instances on the Instances page".
      7. @@ -90,8 +85,7 @@
    - @@ -99,6 +93,7 @@ Dundee, UK
    + +
    +
    + +
    - + +

    JABAWS MANUAL

    @@ -89,17 +90,10 @@ Please note that -r and -f options cannot be used together. Alignment is done wi

    The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but the setting controlling output are not. This is due to the fact the output have to be handled by JABAWS, so must remain within its control. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equal sign. This format is constant no matter which JABAWS web service is used.
    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters

    The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.

    -
    - - - -
    - - - - + + + + +
    +
    + +
    - + +

    JABAWS MANUAL

    @@ -56,10 +57,8 @@
  • Local Engine Configuration
  • Cluster Engine Configuration
  • Executable Configuration
    • -
  • Defining Environment Variables for - Executables
    • -
  • Configure JABAWS to Work -with Mafft
    • +
  • Defining Environment Variables for Executables
    • +
  • Configure JABAWS to Work with Mafft
  • Limiting the size of the job accepted by JABAWS Server
  • Using a different version of the alignment program with JABAWS
  • Load balancing
    • @@ -413,16 +412,10 @@ class="hightlight">log4j.properties and uncomment section of

    Google Analytics can be disabled or adjusted by removing/editing conf/GA.properties Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!

    All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.

    -
    - - -
    - - - - + + + + +
    +
    + +
    - + +

    JABAWS MANUAL

    @@ -351,17 +351,11 @@ For a more detailed description of all available types and their functions pleas

    Building web services artifacts

    JABAWS are the standard JAX-WS SOAP web services, which are WS-I basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as it provides a handful of useful methods in addition to plain data types.

    wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl

    -
    +
    + + + - - - - - - - - +
    +
    + +
    -
    -Home + -
    +

    For JABAWS Developers

    The JABAWS project

    This page is for anyone who wants to add a new webservice into the JABAWS framework.

    @@ -209,12 +209,12 @@ Several testing groups are supported:
  • Test on the cluster.

    •  

    -
    - - +
    +
    + + +
    +
    + +
    - + +

    JABAWS MANUAL

    JABAWS Server Virtual Appliance

    +
  • What is JABAWS Virtual Appliance?
    • +
  • When to use virtual appliance
    • +
  • How to install VMware Player
    • +
  • VMware Player appliance configuration
    • +
  • JABAWS Appliance details
    • +
  • Configuring Jalview to work with your JABAWS VM
    • +
  • VM Network Settings
    • +

     

    What is the JABAWS Server Virtual Appliance?

    The JABAWS Virtual Appliance is a way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. -What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), running an installation of the JABAWS -Web Application Archive (WAR) on TurnKey Linux. Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it.
    -You can run the appliance with freely available program such as VMware Player, but you will need to install it first. We have tested the JABAWS appliance -with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. +What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), +running an installation of the JABAWS Web Application Archive (WAR) on TurnKey Linux. Once this has +started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS +client (such as Jalview or the JABAWS command line client) to connect to it.
    +You can run the appliance with freely available program such as +VMware Player, but you will need to install it +first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and +VMware Fusion on Mac. However, you are not limited to these virtualization systems and can use the JABAWS appliance with any other virtualization platform. You can use VMware OVF tool to prepare JABAWS image for a different virtualization platform e.g. VirtualBox.

    When to use the JABAWS Virtual Appliance

    The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access @@ -136,17 +141,10 @@ but for most production environments, the JABAWS WAR distribution will be easie

    If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.

    VM Network Settings

    By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)

    -
    - - - -
    - - - - + + + + +
    +
    + +
    - + Getting Started + Manual + + Download + Usage Statistics + Services Status + Contact Us + Barton Group +
    + +

    JABAWS MANUAL

    @@ -55,10 +57,8 @@
  • Installing the JABAWS WAR file
  • Preparing executables for use with JABAWS
  • Using the pre-compiled i386 binaries on Linux
    • -
  • Recompiling the bundled - programs for your system
    • -
  • Reuse the binaries that are - already in your system
    • +
  • Recompiling the bundled programs for your system
    • +
  • Reuse the binaries that are already in your system
  • Obtaining command line binaries for your operating system
  • Testing JABAWS Server
  • Running many JABAWS instances on the same server
    • @@ -66,6 +66,7 @@
  • JABAWS supported cluster batch management systems
  • Manually deploying JABAWS application on Apache-Tomcat
    • +

    Troubleshooting

    -
    + + + + - - - - - - - +
    +
    + +
    - + +

    JABAWS MANUAL

    @@ -147,13 +148,9 @@ Each table contains the following information for each web service


    - - +
    - diff --git a/website/manual_qs_amazon.html b/website/manual_qs_amazon.html new file mode 100644 index 0000000..92641ad --- /dev/null +++ b/website/manual_qs_amazon.html @@ -0,0 +1,93 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started + + + + + + +
    + + + + +
    + + + + +
    +

    Getting Started

    +

    Choose a JABAWS distribution

    + + + + + + + + + + + + + + + + + + + + + +
    I want to use JABAWS for...Quick Guide
    Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)
    Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloud
    Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
    Accessing a JABAWS server from my own codeJABAWS Java Client
    + + + +

    Running JABAWS in the Amazon Cloud

    +
      +
    1. Create Amazon Web Services account.
      2. +
    2. Configure JABAWS either on the Amazon EC2 cloud or on Amazon Elastic Beanstalk
      3. +
    +
    +
    + +
    + + + + + + + + + + diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html index 06cca61..b245214 100644 --- a/website/manual_qs_client.html +++ b/website/manual_qs_client.html @@ -2,90 +2,90 @@ - + Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started - +
    +
    + +
    - - + Getting Started + Manual + Download + Usage Statistics + Services Status + Contact Us + Barton Group
    +
    -

    Getting Started

    -

    Choose a JABAWS distribution

    - - - + + - + - - + + - - + +
    I want to use JABAWS for... Quick Guide
    Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)
    Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloud JABAWS on the Amazon cloud
    Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
    Accessing a JABAWS server from my own codeJABAWS Java ClientAccessing a JABAWS server from my own codeJABAWS Java Client
    - -

    The JABAWS command line client

    - -

    This is a single java archive which contains the JABAWS command line client. -It requires Java version 1.6 to run, and allows anyone who wants to connect -to and to use JABAWS from their own software. -You can read more about how to use command line client in the CMD Client section of the manual. -You can also get command line help by changing to the directory where you downloaded the client jar, and typing: -

    +

    + This is a single java archive which contains the JABAWS command line client. It requires Java + version 1.6 to run, and allows anyone who wants to connect to and to use JABAWS from their own + software. You can read more about how to use command line client in + the CMD Client section of the manual. You can also get command line help by changing to + the directory where you downloaded the client jar, and typing: +

    + +

    + A JABA Web Services are WS-I compliant. This means that you can access them from any + language that has libraries or functions for consuming interoperable SOAP web services. + +

    + - + + diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html index 3a6cea8..881caa1 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -2,68 +2,74 @@ - + Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started - +
    +
    + +
    + Getting Started + Manual + Download + Usage Statistics + Services Status + Contact Us + Barton Group
    -
    -

    Getting Started

    +
    +

    Getting Started

    Choose a JABAWS distribution

    - - - + + - + - - + + - - + +
    I want to use JABAWS for... Quick Guide
    Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)
    Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloud JABAWS on the Amazon cloud
    Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
    Accessing a JABAWS server from my own codeJABAWS Java ClientAccessing a JABAWS server from my own codeJABAWS Java Client
    +

    Running JABAWS on your local machine

    -
    • Download JABAWS Virtual Appliance (520M)
      • + -

      The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a virtual machine on your laptop or desktop computer. A complete guide to the JABAWS VA is given in the manual, but for the impatient, a brief instructions are given below: +

      + The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a + virtual machine on your laptop or desktop computer. A complete guide + to the JABAWS VA is given in the manual, but for the impatient, a brief instructions are given below:

      If you work on Windows, Linux or Unix

        @@ -79,16 +85,15 @@
      1. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the Webservices panel and press the New Service URL button.
      2. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.
      -
    - - - - + + + + + +
    +
    +
    + Getting Started + Manual + Download + Usage Statistics + Services Status + Contact Us + Barton Group
    +
    -

    Getting Started

    -

    Choose a JABAWS distribution

    - - - + + - - + + - - + + - - + +
    I want to use JABAWS for... Quick Guide
    Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)
    Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloud Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloud
    Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
    Accessing a JABAWS server from my own codeJABAWS Java ClientAccessing a JABAWS server from my own codeJABAWS Java Client
    - +

    Installing A JABAWS Server Web Application Archive (WAR) package

    - -

    This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.

    +

    + This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable + their local JABA server to use the cluster or perform very large tasks. +

    1. Download the JABAWS WAR for your platform
      2. @@ -100,11 +100,11 @@
    - - + + + +
    + -
    -

    Getting Started

    +
    +

    Getting Started

    Choose a JABAWS distribution

    - - - + + - + - - + + - - + +
    I want to use JABAWS for... Quick Guide
    Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)Running Muptiple Sequence Alignments through Jalview on my own computerJABAWS Virtual Appliance (VA)
    Running JABAWS on the cloud, for one or many usersJABAWS on the Amazon cloudJABAWS on the Amazon cloud
    Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
    Accessing a JABAWS server from my own codeJABAWS Java ClientAccessing a JABAWS server from my own codeJABAWS Java Client
    - - - - -
    - + +
    + +