From: Fábio Madeira Date: Mon, 6 Mar 2017 13:56:48 +0000 (+0000) Subject: JWS-109 & JWS-113 Improved the readability of the getting started guides. Also remove... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fd702a80f520b9593bb24cd5533d57d83d640359;p=jabaws.git JWS-109 & JWS-113 Improved the readability of the getting started guides. Also removed references to the installation of jpred dependencies. --- diff --git a/website/getting_started.jsp b/website/getting_started.jsp index 084da3b..46731e3 100644 --- a/website/getting_started.jsp +++ b/website/getting_started.jsp @@ -15,12 +15,13 @@
-

Choose a JABAWS distribution

+

JABAWS distributions

Choose the JABAWS distribution that better suits your needs and read the quickstart guides below. - Detailed information is available in the JABAWS docs pages. + Detailed information is available in the + JABAWS documentation pages.


@@ -32,18 +33,24 @@ I want to use JABAWS for... + Jalview and the JABAWS Public Server + Running JABAWS services through Jalview on the JABAWS + public server + + JABAWS Virtual Appliance (VA) - Running Multiple Sequence Alignments through Jalview on my - own computer + Running JABAWS services through Jalview on my + computer with a private server JABAWS Web Application aRchive (WAR) Running JABAWS for my group, lab, or organization on the - local infrastructure + local infrastructure - JABAWS Java Client - Accessing a JABAWS server from my own code + JABAWS Command Line Interface (CLI) + Accessing a public or private + JABAWS server from my own software
@@ -53,6 +60,27 @@
+
+
+
+
+

Jalview and the JABAWS Public Server

+
+
+ + +

+ This is the easiest way to run JABAWS web-services. Simply launch + Jalview and run any of the methods + provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default. + If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can + either setup a local JABAWS Virtual Appliance (VA) or + configue the JABAWS Web Application aRchive (WAR) in your infrastructure. +

+
+
+
+
@@ -64,23 +92,24 @@

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: + virtual machine on your laptop or desktop computer. A complete guide + to the JABAWS VA is given in the documentation pages, + but for the impatient, brief instructions are given below:

If you work on Windows, Linux or Unix:

    -
  1. Download JABAWS Virtual Appliance
    2. -
  2. Download and install VMWare Player.
    3. -
  3. Unpack the JABAWS virtual appliance and open it with VMware Player.
    4. +
  4. Download JABAWS Virtual Appliance
    5. +
  5. Download and install VMWare Player
    6. +
  6. 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. + VMware Fusion.

Testing

@@ -93,12 +122,15 @@ Alternatively you can use Jalview to complete the testing.

    -
  1. Launch the desktop version of Jalview
    2. +
  2. Launch the desktop version of Jalview
  3. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the Webservices panel and press the New Service URL button.
  4. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.
+

+ Back to top +

@@ -113,20 +145,21 @@

- 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. + The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization, + or wants to enable their local JABAWS server to use the cluster or perform very large tasks. + Complete documentation is provided in the + documentation pages, but brief instructions are given below:

    -
  1. Download the JABAWS WAR file
    2. -
  2. Download and install Apache-Tomcat.
    - You will need at least Tomcat version 5.5 of - (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6). +
  3. Download the JABAWS WAR file
    4. +
  4. Download and install Apache-Tomcat
    + You will need at least Tomcat version 5.5 of + (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).
  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. + into the webapps directory (if it doesn't, simply unpack the WAR archive).
  8. If you are on Mac or other unix-like architecture with GNU compilers available or you'd like to get a maximum performance
    cd to @@ -151,16 +184,19 @@ jabaws
  9. Alternately, you can point Jalview at your new server: -
      -
    • Launch the desktop version of Jalview
      • +
        +
      1. Launch the desktop version of Jalview
      2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), elect the Webservices panel and press the New Service URL button.
      3. Enter the URL for the tomcat server, including the context path for the JABAWS web app (e.g. http://localhost:8080/jabaws).
        4. -
    +
+

+ Back to top +

@@ -173,21 +209,24 @@

- 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. + This is a single Java archive which contains the JABAWS command line interface (CLI) client. + It allows anyone who wants to connect to the JABAWS web-services running at the + University of Dundee's Public Server, or to run a local private JABAWS server from their own software. + You can read more about how to use JABAWS command line (CLI) client given in the + documentation pages, + but a brief instructions are given below:

    -
  1. Download the Client Jar file
    2. +
  2. Download the Client Jar file
    3. +
  3. Download and install Java + (version 1.6)
    4. +
  4. Provided that you have the Java ready to run, you can get command line help by changing to + the directory where you downloaded the client jar, and typing:
    + 
    java -jar jaba-client.jar
    +

- 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 JABA Web Services are WS-I compliant. This means that you can access them from any + The 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.