From c219257fd9512af182cd65ab5bda8d3dc7ef12c6 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Thu, 11 Aug 2011 12:56:46 +0000 Subject: [PATCH] Adding new web service, getting rid of virtual box in docs git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4491 e3abac25-378b-4346-85de-24260fe3988d --- website/download.html | 15 ++++++++------- website/index.html | 2 +- website/man_about.html | 3 ++- website/man_client.html | 2 +- website/man_dev.html | 14 +++++++++++++- website/man_serverwar.html | 12 ++++++------ website/manual_qs_va.html | 5 ----- 7 files changed, 31 insertions(+), 22 deletions(-) diff --git a/website/download.html b/website/download.html index fe56e7d..88923df 100644 --- a/website/download.html +++ b/website/download.html @@ -38,7 +38,7 @@ page

JABAWS Server Virtual Machine

-

JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend VMWare Player for Windows and Linux users. There is also an Oracle VirtualBox (version 3.2.12) for Mac users. Both are free and installation is simple. Jalview can use your local JABAWS VM.

+

JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend VMWare Player for Windows and Linux users or VMware Fusion for Mac users. Jalview can use your local JABAWS VM.

@@ -46,11 +46,12 @@ page

JABAWS Server Web Application

-

The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. Typically, you will have a cluster or at least a powerful server machine which all users are willing to use. If you only have a single server then, you may use JABAWS Server Virtual Appliance instead. The server is provided as a self-contained Web Application -aRchive (WAR) containing all necessary binaries. WAR file can be deployed on any - web application server -supporting at least version 2.4 of the Java servlet specification, i.e. Tomcat 7.0.

- +

The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. You can also use this version for Mac and Linux computers if you do not want to use virtualization. Finally, you can use this version with a cluster.
+ The server is provided as a self-contained Web Application + aRchive (WAR) containing all necessary binaries. WAR file can be deployed on any + web application server + + supporting at the Java servlet specification v. 2.4 or above, i.e. Tomcat 7.0.

-

Please bear in mind that if you deploy JABAWS WAR on Windows, only the Muscle and Clustal web services will work! If you want to run the other web services on Windows, then use the JABAWS Server VM package instead. +

Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VM package instead.

diff --git a/website/index.html b/website/index.html index e8713c4..35cb029 100644 --- a/website/index.html +++ b/website/index.html @@ -39,7 +39,7 @@ page

JABAWS 2

-

JABAWS2.0:Disorder is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are based on DisEMBL, IUPred, Ronn, GlobPlot, conservation is calculated by AACon, multiple sequence alignment services are the Clustal W, JABAWS2.0:Disorder is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are based on DisEMBL, IUPred, Ronn, GlobPlot, conservation is calculated by AACon, multiple sequence alignment services are the Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. JABA Web Services can be accessed from the Jalview multiple sequence alignment editor and analysis workbench to allow multiple alignment calculations limited only by your own local computing resources.

diff --git a/website/man_about.html b/website/man_about.html index bea4ae6..ae8e300 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -75,7 +75,8 @@

JABAWS currently provides access to the following programs:

Multiple Sequence Alignement

    -
  • ClustalW (version 2.0.12)
    • +
  • Clustal Omega (version 1.0.2)
    • +
  • ClustalW (version 2.0.12)
  • Mafft (version 6.857)
  • Muscle (version 3.8.31)
  • Tcoffee (version 8.99)
    • diff --git a/website/man_client.html b/website/man_client.html index 5738114..a4b13de 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -52,7 +52,7 @@

    The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

    Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
    -h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
    --s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS] +-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]


    ACTIONS:
    diff --git a/website/man_dev.html b/website/man_dev.html index 491ebc5..2abadaf 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -140,12 +140,24 @@ + "Port"), MsaWS.class);

    Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from the javadoc.

    Valid JABAWS service names and WSDL files

    -
      +

      Multiple sequence alignment services

      +
      • ClustalOWS (http://www.compbio.dundee.ac.uk/jabaws/ClustalOWS?wsdl)
      • ClustalWS (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl)
      • MuscleWS (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl)
      • MafftWS (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl)
      • TcoffeeWS (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl)
      • ProbconsWS (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl)
        • +
      +

      Protein disorder prediction services

      +
        +
      • IUPredWS (http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl)
        • +
      • GlobPlotWS (http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl)
        • +
      • DisEMBLWS (http://www.compbio.dundee.ac.uk/jabaws/DisEMBLWS?wsdl)
        • +
      • JronnWS (http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl)
        • +
      +

      Amino acid conservation service

      +
        +
      • AAConWS (http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl)

      Aligning sequences

      Given that msaws is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows:

      diff --git a/website/man_serverwar.html b/website/man_serverwar.html index 61801cf..0dc1ce3 100644 --- a/website/man_serverwar.html +++ b/website/man_serverwar.html @@ -57,8 +57,7 @@ programs for your system
    • Reuse the binaries that are already in your system
      • -
    • Obtaining alignment - programs for your operating system
      • +
    • Obtaining command line binaries for your operating system
    • Testing JABAWS Server
    • Running many JABAWS instances on the same server
    • JABAWS on a single server
      • @@ -185,8 +184,7 @@ Then the default configuration will work for you. More information about the Executable.properties file is given in the JABAWS Configuration chapter.

      -

      Obtaining alignment -programs for your operating system

      +

      Obtaining command line binaries for your operating system

      You could search for pre-packaged compiled executable in your system package repository or alternately, download pre-compiled @@ -195,11 +193,13 @@ replace the executables supplied with the downloaded ones, or modify the paths in executable.properties as described above. Below are some suggestions on where you may be able to get the binaries for your system.

      Testing JABAWS Server

      First of all make sure that Tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your Tomcat JABAWS context path e.g. http://myhost.compbio.ac.uk:8080/jabawsIf you see it, then it is time to make sure that web services are working too. Assuming that you have unpacked/deployed JABAWS from the server war file, you should be able to navigate to the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type: java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path>

      @@ -243,7 +243,7 @@ modify the paths in - diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html index be95fc1..7a62a41 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -65,11 +65,6 @@
    • download and install VMWare Player.
    • Unpack the JABAWS virtual appliance and open it with VMware Player.
      • -

      If you use a Mac, or prefer not to use VMWare, then :

      -
        -
      1. download and install Virtual Box.
        2. -
      2. Unpack the JABAWS virtual appliance, import it into VirtualBox and then start the appliance.
        3. -

      Testing

      The easiest way to test that your JABAWS Virtual appliance is working is to use Jalview.

      -- 1.7.10.2