From: Jim Procter Date: Mon, 1 Jul 2013 14:14:16 +0000 (+0100) Subject: Merge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalvie... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5e7cd807ed94d8e176375f183430ae3977825876;hp=65f579f3a0ff4e2626017be25f015ee5c6e39275;p=jabaws.git Merge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_1 Conflicts: website/man_about.html Tweaked the wording a bit more - introduced standard man_about.html#jabaX.Y.Z style name anchor for update history --- diff --git a/website/contacts.html b/website/contacts.html index dce1e20..a238e47 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -1,4 +1,4 @@ - + @@ -51,7 +51,7 @@ - + diff --git a/website/develhome.html b/website/develhome.html index 4ac519d..53395fc 100644 --- a/website/develhome.html +++ b/website/develhome.html @@ -110,7 +110,7 @@ Several testing groups are supported:

http://www.compbio.ac.uk:8080/ws

JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible.

- + diff --git a/website/index.html b/website/index.html index c60ab98..532c5d1 100644 --- a/website/index.html +++ b/website/index.html @@ -41,19 +41,18 @@

JABAWS 2.0.1

JABAWS -is free software which provides web services for multiple sequence alignment -(programs available: Clustal Omega, Clustal W, +is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment +include 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. +TCOFFEE and PROBCONS. Analysis services allow +prediction of protein disorder with DisEMBL, IUPred, +Ronn and GlobPlot; +and calculation of amino acid alignment conservation with AACon. +

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

+JABA 2.0.1 Web Services installations can be accessed from the Jalview desktop application (version 2.8 onwards) and the JABAWS command-line client, and provide multiple alignment +and sequence analysis calculations limited only by your own computing resources.
+

@@ -115,13 +114,11 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel= 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

-

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. -

+

We advise you to update to JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and + contains some important bug fixes. Please consult the manual for more information + on compatibility between versions.

Should you require them, however, old versions of JABAWS are available here:

Reference

Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for diff --git a/website/man_about.html b/website/man_about.html index 1f55cbc..f0c9b53 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -72,7 +72,6 @@ (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 @@ -85,18 +84,17 @@

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.
    • -
  • 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.
    • +
  • 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.
    • +
  • 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.
-

JABA Web Services Programs

-

JABAWS currently provides access to the following programs:

+

JABAWS currently provides access to the following programs:

Multiple Sequence Alignement

  • Clustal Omega (version 1.0.2)
    • @@ -118,20 +116,33 @@ - -

    What is new in JABAWS 2.0.1?

    -

    This release of JABAWS 2.0.1 is mostly bug fixing release. This is a list of bugs which have been fixed in JABAWS 2.0.1:

    +

    What is new in JABAWS 2.0.1?

    +

    JABAWS Version 2.0.1 includes several minor updates and bug fixes for JABAWS Version 2. These are listed below:

    • Disembl returned swapped strings for HOTLOOPS and REM465
    • Jronn failed to process jobs with more than 3 sequences
      • -
    • JABAWS could not deal with FASTA records with the '>' symbols in the record identificator
      • +
    • JABAWS could not deal with FASTA records with '>' symbols in the record identificator
    • Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
    • JABAW never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties
    • Default web security has been incompatible with Tomcat 7.0.31 and newer
    + JABAWS Version 2 (Released 16th Dec 2011)

    Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease 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
      • +
    • web services execution statistics visualization
      • +
    • 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
      • +

    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 @@ -143,14 +154,12 @@ 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 2.0.1 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. + v2.0 clients should also be able to use JABAWS 2.0.1 services. To access the analysis web services introduced in + JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must 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 @@ -161,9 +170,8 @@ This package is based on the autogenerated source code produced by data model javadoc.

    - - + diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 15fdd88..822ec3b 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -68,7 +68,7 @@

    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 index 637996e..004da8b 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -71,7 +71,7 @@

     

    - + diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html index 1ab14c1..8313b9b 100644 --- a/website/man_awscloud_ec2.html +++ b/website/man_awscloud_ec2.html @@ -84,7 +84,7 @@

     

    - + diff --git a/website/man_client.html b/website/man_client.html index 66550b0..a3f7718 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -87,11 +87,11 @@ Please note that -r and -f options cannot be used together. Alignment is done wi --fastaparttree
    --retree=10
    --op=2.2

    -

    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.
    +

    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 because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. 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 equals 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.

    - + diff --git a/website/man_configuration.html b/website/man_configuration.html index 2ce17a8..d60ecb8 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -413,7 +413,7 @@ 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.

    - + diff --git a/website/man_dev.html b/website/man_dev.html index 2c41932..bdd050c 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -352,7 +352,7 @@ For a more detailed description of all available types and their functions pleas

    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

    - + diff --git a/website/man_server_dev.html b/website/man_server_dev.html index 993589c..f5ef11b 100644 --- a/website/man_server_dev.html +++ b/website/man_server_dev.html @@ -210,7 +210,7 @@ Several testing groups are supported:

     

    - + diff --git a/website/man_servervm.html b/website/man_servervm.html index 4c6d349..b96a9c1 100644 --- a/website/man_servervm.html +++ b/website/man_servervm.html @@ -142,7 +142,7 @@ but for most production environments, the JABAWS WAR distribution will be easie

    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)

    - + diff --git a/website/man_serverwar.html b/website/man_serverwar.html index 11fb7e7..4445f07 100644 --- a/website/man_serverwar.html +++ b/website/man_serverwar.html @@ -236,7 +236,7 @@ modify the paths in If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.
- + diff --git a/website/man_stats.html b/website/man_stats.html index 356ce90..5574c60 100644 --- a/website/man_stats.html +++ b/website/man_stats.html @@ -148,7 +148,7 @@ Each table contains the following information for each web service


- + diff --git a/website/manual_qs_amazon.html b/website/manual_qs_amazon.html index 780814b..c132212 100644 --- a/website/manual_qs_amazon.html +++ b/website/manual_qs_amazon.html @@ -71,7 +71,7 @@ - + diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html index f8396ea..31dff99 100644 --- a/website/manual_qs_client.html +++ b/website/manual_qs_client.html @@ -82,7 +82,7 @@

- + diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html index 7db41ee..91d2774 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -88,7 +88,7 @@ - + diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html index 470122f..875a528 100644 --- a/website/manual_qs_war.html +++ b/website/manual_qs_war.html @@ -99,7 +99,7 @@ - + diff --git a/website/quick_start.html b/website/quick_start.html index bb866a6..5a384e1 100644 --- a/website/quick_start.html +++ b/website/quick_start.html @@ -59,7 +59,7 @@
- +