From 85f830bbd51a7277994bd4233141016304e210c9 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Fri, 12 Aug 2011 12:36:42 +0000 Subject: [PATCH] website docs update git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4501 e3abac25-378b-4346-85de-24260fe3988d --- website/contacts.html | 2 +- website/download.html | 22 ++++++++++++---------- website/index.html | 8 ++++---- website/man_about.html | 4 ++-- website/man_client.html | 2 +- website/man_configuration.html | 2 +- website/man_dev.html | 7 ++++--- website/man_servervm.html | 2 +- website/man_serverwar.html | 7 ++++--- website/man_stats.html | 5 ++++- website/manual_qs_client.html | 7 +++---- website/manual_qs_va.html | 3 ++- website/manual_qs_war.html | 16 +++++++++------- website/quick_start.html | 2 +- 14 files changed, 49 insertions(+), 40 deletions(-) diff --git a/website/contacts.html b/website/contacts.html index d9b49b1..6ef67db 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -51,7 +51,7 @@ page - - diff --git a/website/man_dev.html b/website/man_dev.html index 2abadaf..3e5a373 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -152,13 +152,14 @@

Amino acid conservation service

+ +

Please replace http://www.compbio.dundee.ac.uk/ with your JABAWS instance host name, and jabaws with your JABAWS context name to access your local version of JABAWS web services. For example http://localhost:8080/jabaws would be a valid URL for the default Apache-Tomcat installation and jabaws.war file deployment.

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:

1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
@@ -351,7 +352,7 @@ For a more detailed description of all available types and their functions pleas -

diff --git a/website/man_servervm.html b/website/man_servervm.html index e24e333..a28e486 100644 --- a/website/man_servervm.html +++ b/website/man_servervm.html @@ -67,7 +67,7 @@ What the appliance provides is a 'virtual server machine' (or more simply - virt 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 convert JABAWS image to a different virtualization format e.g. OVF.

+ 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 systems over an internet, or just want to keep their data private. It is also diff --git a/website/man_serverwar.html b/website/man_serverwar.html index 0dc1ce3..af1fcf4 100644 --- a/website/man_serverwar.html +++ b/website/man_serverwar.html @@ -73,12 +73,13 @@ version 2.4 of the Java Servlet specification, and a Java 6 runtime environment. We recommend using an official Oracle Java 6 runtime environment, and Apache-Tomcat web application server version 6, but other versions may work as well.
Please Note: The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.

+href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat web application server version 7, but older Tomcat versions above 5.5 would work too.
+Please Note: The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.

-

JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform. +

JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, not all web services are currently available for MS Windows platform.

-

JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries, as well as the source code and build scripts necessary to recompile them.

+

JABAWS comes with pre-compiled MS Windows and Linux x86 binaries, as well as the source code and build scripts necessary to recompile them.

To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes.

Installing the JABAWS WAR file

JABAWS is distributed as a web application archive (WAR). To diff --git a/website/man_stats.html b/website/man_stats.html index da8036f..6e2c802 100644 --- a/website/man_stats.html +++ b/website/man_stats.html @@ -51,6 +51,7 @@

JABAWS Usage Statistics

The summary for each column is displayed in the last row of the table.

+

Authentication

+

Authentication lets you see the detailed usage statistics. If you are using JABAWS VA (Virtual Appliance) then the username is jabaws and password is not defined, e.g. empty. In other cases you need to ask your system administrator for it.

Detailed Usage Statistic

Detailed execution statistics for each month is available for authenticated users only.

JABAWS one month usage statistics

@@ -144,7 +147,7 @@ Each table contains the following information for each web service - diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html index 1f7c595..116f548 100644 --- a/website/manual_qs_client.html +++ b/website/manual_qs_client.html @@ -64,15 +64,14 @@ -

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:

+
  • java -jar jaba-client.jar
    • +

    A JABAWS server's 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.

    @@ -80,7 +79,7 @@ language that has libraries or functions for consuming interoperable SOAP web se - diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html index 7a62a41..dac6368 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -65,6 +65,7 @@
  • download and install VMWare Player.
  • Unpack the JABAWS virtual appliance and open it with VMware Player.
    • +

    If you work on Mac do the same using VMware Fusion, or for free alternative use a WAR JABAWS package.

    Testing

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

    @@ -78,7 +79,7 @@
    - diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html index 9fbc23c..481d802 100644 --- a/website/manual_qs_war.html +++ b/website/manual_qs_war.html @@ -64,15 +64,17 @@

    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 with all binaries (45M)
      2. -
    2. Download and install Apache-Tomcat.
      - You will need at least version 5.5 of Tomcat (we would recommend version 6.0) and at least version 1.6 (i.e. JAVA 6) of Java.
      3. +
    3. Download the JABAWS WAR for your platform
      4. +
    4. Download and install Apache-Tomcat.
      + You will need at least version 5.5 of Tomcat (we would recommend version 7.0) and at least version 1.6 (i.e. JAVA 6) of Java.
    5. Drop the JABAWS WAR file into tomcat/webapps directory.
    6. (Re)start the Tomcat.
    7. Once the tomcat has started, it should automatically unpack the WAR into the webapps directory (if it doesn't, then you'll need to do this manually, it's just a zip archive in the end).
    8. You then need to complete the installation of the executable binaries:
      9. -