From: pvtroshin Date: Fri, 16 Sep 2011 14:39:42 +0000 (+0000) Subject: web site update new pages for awss beanstalk deployment X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a2cffcf92327725d8fc8abfd49d032176be4e86a;p=jabaws.git web site update new pages for awss beanstalk deployment git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4591 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/contacts.html b/website/contacts.html index 6ef67db..faee9ad 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -29,8 +29,9 @@ page Getting Started Manual Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -51,7 +52,7 @@ page - - + diff --git a/website/download.html b/website/download.html index 5feb188..bb430c3 100644 --- a/website/download.html +++ b/website/download.html @@ -30,8 +30,9 @@ page Getting Started Manual Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -107,7 +108,7 @@ page - @@ -51,7 +52,7 @@ page

For Users

The Server: JABAWS Virtual Appliance: (520M) - or JABAWS AMI for the Amazon EC2 Cloud
+ 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!

@@ -106,7 +107,7 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel= - diff --git a/website/man_about.html b/website/man_about.html index 8532f8c..e26dbdf 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -38,8 +38,9 @@ JABAWS Development Download - Contact Us Usage Statistics + Services Status + Contact Us Barton Group @@ -117,7 +118,7 @@ but in addition, offers some additional methods which simplify working with JABA - diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 24a07e1..2737cd6 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -45,8 +45,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -57,8 +58,9 @@

JABAWS Server in the Amazon Cloud

+
  • How to use JABAWS on the Amazon EC2 cloud
    • +
  • How to use JABAWS WAR on Amazon Elastic Beanstalk
    • +

    JABAWS on the Cloud

    We provide pre-configured JABAWS Amazon Machine Image (AMI) which you can use on the Amazon EC2 cloud. Typical use cases are

    @@ -67,43 +69,13 @@
  • your organization already uses the Amazon cloud and you do not want to do any special arrangements for the JABAWS
  • you want to benefit from the Amazon automatic scaling and monitoring to make sure JABAWS is always ready
    • -

    If you know what to do than JABAWS AMI ID is ami-40fecd34, manifest 846107356395/JABAWS2 to get you started, if not read on.

    -

    How to use JABAWS on the Amazon EC2 cloud

    -
      -
    1. Create Amazon Web Services account.
      2. -
    2. 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.
      3. -
    3. Click on "Launch Instance" button marker 2.
      4. - -AWS console -
    4. Go to the "Community AMI" tab and search for JABAWS, then click select.
      5. -select AMI -
    5. Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs. If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen the hardware click continue.
      6. - - select hardware - -
    6. You should not need to customize anything on this page, continue to the next.
      7. - - keys - -
    7. At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH.
      8. - - -
    8. 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).
      9. - - ese -
    9. Review the configuration and launch the instance, then click "view your instances on the Instances page".
      10. - -
    10. At this point you should have JABAWS instance up and running. Your AWS console should look something like this:
      11. - -
    11. Now you can consume JABAWS web services by accessing the public DNS address of your JABAWS server instance. For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public DNS address with http:// e.g. type: http://<public DNS>. The JABAWS instance on the screenshot can be accessed on http://ec2-46-137-50-196.eu-west-1.compute.amazonaws.com.
      12. -
    -

    If you need to run JABAWS for large organization you might want to configure load balancer and auto scaling. Please get in contact with us if you are interested in exploring such configurations.

    -

     

    -
    +

    If you know what to do than JABAWS AMI ID is ami-40fecd34, manifest 846107356395/JABAWS2 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.

    + + - - diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html new file mode 100644 index 0000000..44180fb --- /dev/null +++ b/website/man_awscloud_bs.html @@ -0,0 +1,100 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual + + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    How to use JABAWS on Amazon Elastic Beanstalk

    +
    +
      +
    1. Create Amazon Web Services account.
      2. +
    2. Log in into the Amazon Web Services (AWS) console and switch to AWS Elastic Beanstalk view.
      3. + Elastic Beanstalk launch JABAWS war step 1 +
    3. Create a new Beanstalk application by uploading JABAWS war file
      4. + Elastic Beanstalk launch JABAWS war step 2 +
    4. Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS.
      5. + Elastic Beanstalk launch JABAWS war step 3 + +
    5. Choose the type of hardware you want to run JABAWS on.
      6. +Elastic Beanstalk launch JABAWS war step 4 +
    6. If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com
      7. +Elastic Beanstalk launch JABAWS war +
    +

     

    +
    +
    + + +
    + + +
    + + + + + + + + diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html new file mode 100644 index 0000000..7fe85ff --- /dev/null +++ b/website/man_awscloud_ec2.html @@ -0,0 +1,115 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual + + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    How to use JABAWS on the Amazon EC2 cloud

    +
    +
      +
    1. Create Amazon Web Services account.
      2. +
    2. 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.
      3. +
    3. Click on "Launch Instance" button marker 2.
      4. + +AWS console +
    4. Go to the "Community AMI" tab and search for JABAWS, then click select.
      5. +select AMI +
    5. Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs. If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen the hardware click continue.
      6. + + select hardware + +
    6. You should not need to customize anything on this page, continue to the next.
      7. + + keys + +
    7. At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH.
      8. + + +
    8. 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).
      9. + + ese +
    9. Review the configuration and launch the instance, then click "view your instances on the Instances page".
      10. + +
    10. At this point you should have JABAWS instance up and running. Your AWS console should look something like this:
      11. + +
    11. Now you can consume JABAWS web services by accessing the public DNS address of your JABAWS server instance. For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public DNS address with http:// e.g. type: http://<public DNS>. The JABAWS instance on the screenshot can be accessed on http://ec2-46-137-50-196.eu-west-1.compute.amazonaws.com.
      12. +
    +

    If you need to run JABAWS for large organization you might want to configure load balancer and auto scaling. Please get in contact with us if you are interested in exploring such configurations.

    +

     

    +
    +
    + + +
    + + +
    + + + + + + + + diff --git a/website/man_client.html b/website/man_client.html index a0b7862..7b106bc 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -91,7 +92,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi - diff --git a/website/man_configuration.html b/website/man_configuration.html index 00857d6..7a126d9 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -207,7 +208,7 @@ can access and execute them.

    just pass whatever is specified in this line directly to the cluster submission library. This is how DRMAA itself treats this settings. More exactly DRMAA JobTemplate.setNativeSpecification() function will be called.

    - +

    For further details and examples of configuration please refer to the Executable.properties file supplied with JABAWS.

    Defining Environment Variables for Executables

    @@ -257,13 +258,14 @@ defined in Limiting the size of the job accepted by JABAWS

    JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and prevents waist of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. Furthermore, you can define different limits for different presets of the same web service.
    -By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.

    +By default limits are disabled. You can enable them by editing conf/Executable.properties file. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.

    Using a different version of the alignment program with JABAWS

    JABAWS supplied with binaries and source code of the executables which version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable supported. This could be the case with more recent executable. If the options supported by your chosen executable is different when the standard JABAWS executable, than you need to edit ExecutableNameParamaters.xml  configuration file.

    Load balancing

    If your cluster is busy and have significant waiting times you can achieve a faster response by allowing the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit "# LocalEngineExecutionLimit #" preset in <ServiceName>Limits.xml file accordingly. JABAWS server then will balance the load according to the following rule: If the task size is smaller then the maximum task size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit the task to the cluster.

    Testing JABA Web Services

    -

    You can use a command line client (part of the client only +

    Access <your_JABAWS_server_URL>/ServiceStatus to test all web services. Each time you access this URL, all services are tested. You can test a particular web service by adding its name at the end of this URL. For example http://localhost:8080/jabaws/ServiceStatus/MuscleWS will test MuscleWS webservice only. For production configuration we recommend prohibiting requests to this URL for non authenticated users to prevent excessive load on the server.

    +

    Alternatively, you can use a command line client (part of the client only package) to test your JABAWS installation as described here. If you downloaded a JABAWS server package, you can use <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar to test JABAWS installation as described in log4j.properties and uncomment section of name of the executable + ExecutionStatistics + The database for storing the execution statistics. + + + statpages + Web pages for usage statistics visialization and webservices status queries. + + jobsout/ Contains directories generated when running an individual executable. E.g. input and output files and some other task related data. (optional) @@ -352,6 +362,10 @@ class="hightlight">log4j.properties and uncomment section of binaries. + binaries/windows + Contains binaries for MS Windows operating system. + + binaries/matrices Substitution matrices @@ -391,7 +405,7 @@ class="hightlight">log4j.properties and uncomment section of -

    diff --git a/website/man_dev.html b/website/man_dev.html index f5c087c..5180eec 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -353,7 +354,7 @@ For a more detailed description of all available types and their functions pleas - diff --git a/website/man_server_dev.html b/website/man_server_dev.html index a40fd96..2a3f246 100644 --- a/website/man_server_dev.html +++ b/website/man_server_dev.html @@ -39,8 +39,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -210,7 +211,7 @@ Several testing groups are supported:

     

    - diff --git a/website/man_servervm.html b/website/man_servervm.html index 952d716..53391de 100644 --- a/website/man_servervm.html +++ b/website/man_servervm.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -138,7 +139,7 @@ but for most production environments, the JABAWS WAR distribution will be easie - diff --git a/website/man_serverwar.html b/website/man_serverwar.html index 57e54a1..ddd7204 100644 --- a/website/man_serverwar.html +++ b/website/man_serverwar.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -108,28 +109,13 @@ configuration files so these are used instead.

    Using the pre-compiled i386 binaries on Linux

    -

    Before the binaries that are bundled with JABAWS can be used, -they must first be made executable using the provided 'setexecflag.sh' script:

    - -
      -
    1. cd to <webapplicationpath>/binaries/src
      2. - -
    2. run sh setexecflag.sh
      3. - -
    3. Make sure binaries supplied work under your OS.
      - For this run each binary, without any command line options or +

      JABAWS comes with pre-compiled x86 Linux binaries, thus on such systems JABAWS should work straight out of the box. If you are in any doubts or experience problems you may want to make sure that the binaries supplied work under your OS. To do this just execute each binary, without any command line options or input files. If you see an error message complaining about missing libraries or other problems, then you probably need to recompile the binaries.

      4. - -
    4. Restart the Tomcat.
      5. -
    +"#recompbinaries">recompile the binaries.

    -That's it! JABAWS should work at this point. Try it out using the JABAWS test client. If not, -read on... or have a look at deploying on Tomcat tips.
    +You can try the JABAWS functionality with the JABAWS test client or have a look at deploying on Tomcat tips if you experience any problems.
    Note: You may want to enable logging, as described here.
    @@ -204,7 +190,8 @@ modify the paths in IUPred (Linux x86 | x64 | Mac)

    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>

    +

    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. The easiest way to do so is to access ServiceStatus web page.

    +

    Alternatively, you should be able to use 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>

    For example to test all JABAWS web services on host myhost.compbio.ac.uk type:

    java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws

    You can choose a particular web server using -s option like this java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory.

    @@ -245,7 +232,7 @@ modify the paths in - diff --git a/website/man_stats.html b/website/man_stats.html index a84aa7f..1673c5b 100644 --- a/website/man_stats.html +++ b/website/man_stats.html @@ -40,8 +40,9 @@ JABAWS Development Download -Contact Us Usage Statistics +Services Status +Contact Us Barton Group @@ -148,7 +149,7 @@ 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 8033191..f5ff600 100644 --- a/website/manual_qs_client.html +++ b/website/manual_qs_client.html @@ -25,8 +25,9 @@ Getting Started Manual Download - Contact Us Usage Statistics + Services Status + Contact Us Barton Group @@ -48,7 +49,7 @@ Running JABAWS on the cloud, for one or many users - JABAWS AMI + JABAWS on the Amazon cloud Running JABAWS for my group, lab, or organization on the local infrastructure @@ -83,7 +84,7 @@ 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 6810163..7c5de4f 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -25,8 +25,9 @@ Getting Started Manual Download - Contact Us Usage Statistics + Services Status + Contact Us Barton Group
    @@ -46,7 +47,7 @@ Running JABAWS on the cloud, for one or many users - JABAWS AMI + JABAWS on the Amazon cloud Running JABAWS for my group, lab, or organization on the local infrastructure @@ -72,9 +73,9 @@

    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.

    -
      -
    1. Launch the desktop version of Jalview
      2. +

      To check that your JABAWS virtual appliance is working visit the Services Status page available from the main JABAWS menu. For this enter the JABAWS URL for your new server into a web browser. This is shown once the appliance is booted up.

      +

      Alternatively you can use Jalview to complete the testing.

      +
      1. Launch the desktop version of Jalview
      2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the Webservices panel and press the New Service URL button.
      3. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.
      @@ -83,7 +84,7 @@
    -
    diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html index 5dc65c3..9ce3951 100644 --- a/website/manual_qs_war.html +++ b/website/manual_qs_war.html @@ -26,8 +26,9 @@ Getting Started Manual Download - Contact Us Usage Statistics + Services Status + Contact Us Barton Group @@ -49,7 +50,7 @@ Running JABAWS on the cloud, for one or many users - JABAWS AMI + JABAWS on the Amazon cloud Running JABAWS for my group, lab, or organization on the local infrastructure @@ -74,24 +75,25 @@
  • Drop the JABAWS WAR file into tomcat/webapps directory.
  • (Re)start the Tomcat.
  • 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).
    • -
  • You then need to complete the installation of the executable binaries:
    • +
  • You then need to complete the installation of the executable binaries (this is optional if you use 32 bit version of Linux):
    • If you are on Linux or Mac (OSX intel Mac only)
      cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script to ensure the JABAWS binaries can be executed.
      • -
    • If you are on other unix-like architecture with gnu compilers available or you'd like to get a maximum performance:
      • -
    • cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on.
      • -
    • cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script.
      • -
    +
  • If you are on other unix-like architecture with gnu compilers available or you'd like to get a maximum performance:
    • +
  • cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on.
    • +
  • cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script.
    • +

    Testing

    -

    You can test that your JABAWS server is working in two ways.

    +

    You can test that your JABAWS server is working in several ways.

      +
    1. Visit Services Status page available from the main menu using your web browser.
      2. +
    2. If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running: -java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws -In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws + java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws + In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws
      3. -
    3. Alternately, you can point Jalview at your new server:
      • Launch the desktop version of Jalview
        • @@ -103,7 +105,7 @@ In this example we assumed that your JABAWS server URL is Last update: 10 August 2011
        + diff --git a/website/quick_start.html b/website/quick_start.html index b7cc4b8..242c148 100644 --- a/website/quick_start.html +++ b/website/quick_start.html @@ -25,8 +25,9 @@ Getting Started Manual Download - Contact Us Usage Statistics + Services Status + Contact Us Barton Group @@ -47,7 +48,7 @@ Running JABAWS on the cloud, for one or many users - JABAWS AMI + JABAWS on the Amazon cloud Running JABAWS for my group, lab, or organization on the local infrastructure @@ -66,7 +67,7 @@ -