Prequips:Eclipse Setup

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 +This page describes how to set up Eclipse to modify or add features of [[Prequips]].
 +
== Required Eclipse Features == == Required Eclipse Features ==
 +You will need the following Eclipse features to build and launch Prequips:
 +
 +# Eclipse Project SDK 3.1.2 - 3.2.1 (download from http://www.eclipse.org or a mirror site)
 +# EMF SDK 2.1.2 - 2.2.1(download manually the EMF-SDO-XSD build. The update site is: http://download.eclipse.org/tools/emf/updates/site.xml)
 +# Subclipse to access the Subversion repository (update site: http://subclipse.tigris.org/update/site.xml,
 +or use latest unstable: http://subclipse.tigris.org/update_1.2.x)
 +
 +=== Getting the Eclipse Project SDK ===
 +
 +Go to http://www.eclipse.org/downloads/index_project.php and select '''Platform''' under '''Eclipse Project'''. On the next page select build (tested for 3.1.2 - 3.2.1).
 +
 +Download the archive and extract it into a directory of your choice. Your Eclipse installation can live within that directory and there's no need to have administrator privileges to set up the software.
 +
 +=== Installing Features From Within Eclipse ===
 +
 +Once you have downloaded and set up the Eclipse Project SDK you can use the Eclipse Update Manager to add the other features. Simply go to '''Help > Software Updates > Find and Install ...'''. Select '''Search for new features to install''' and then select '''New Remote Site ...'''. Enter a name and the corresponding update site URLs. Then select the latest version of the feature and install. (NOTE, that had to install EMF manually
 +to get the version that also contained XSD)
== Subversion Repository == == Subversion Repository ==
 +Prequips source code can be retrieved from the Subversion repository located at http://db.systemsbiology.net/svn/ngehlenb. To browse the repository comfortably use http://db.systemsbiology.net/cgi-bin/ngehlenb-cgi/viewcvs/viewcvs.cgi.
 +
 +'''Access:''' The repository is no longer world-accessible. If you want to read from or write to the repository please contact [mailto:ngehlenborg@systemsbiology.org Nils Gehlenborg].
 +
 +== Checking Out the Main Application ==
 +
 +After you have installed the Subclipse plug-in go to '''Window > Open Perspective > Other ...''' and select '''SVN Repository Exploring'''. Right-click in the '''SVN Repository''' tab and go to '''New > Repository Location ...'''. Enter the repository location shown in the previous section and click '''Finish'''.
 +
 +A list of projects will show up in the view. Select the '''prequips_core''' project and right-click it. Select '''Checkout ...''' and then '''Check out as project configured using the New Project Wizard'''. ''Don't select the other option, it will get you into trouble when you try to build the project.''
 +
 +Click on '''Finish''' and then select '''Plug-in Project''' under '''Plug-in Development''' in the New Project Wizard. Enter '''prequips_core''' or something similar as project name and click '''Next'''. On the next page click '''Finish'''. All project settings will be imported from the repository. There is no need to enter anything.
 +
 +== Checking Out the prequips_external ==
 +
 +prequips_external holds 3rd party libraries such as log4j
 +and xerces. These libraries are needed by MSXMLParser
 +
 +Open the SVN repository perspective again
 +(Window -> Open Perspective -> Other -> SVN Repository Exploring)
 +
 +Right click on prequips_external
 +
 +Select Checkout
 +
 +Select "Check out as a project in the workspace"
 +
 +Select Finish
 +
 +== Add prequips_external to Java Build Path Libraries ==
 +
 +Open the Java perspective
 +(Window -> Open Perspective -> Java)
 +
 +Right click on prequips_core
 +
 +Select Build Path --> Configure Build Path
 +
 +Select the "Libraries" tab in the new window
 +
 +Select "Add Class folder"
 +
 +Check prequips_external and then select "Okay"
 +
 +
 +== Check out peptideXML and peptideXML.feature ==
 +
 +Open the SVN repository perspective
 +(Window -> Open Perspective -> Other -> SVN Repository Exploring)
 +
 +Right click on peptideXML
 +
 +Select "Checkout as a project configured using the New Project Wizard",
 +then "finish"
 +
 +Select "Plugin Project" from the New Project Wizard panel
 +
 +Use "peptideXML" as the project name, then "Next", then "Finish"
 +
 +In the SVN repository perspective, right click on peptideXML.feature
 +
 +Select "Checkout as a project configured using the New Project Wizard"
 +
 +In the New Project Wizard panel, open the Plug-in development folder,
 +and select "Feature Project"
 +
 +Enter peptideXML.feature as the Project Name and select "Finish"
 +
 +== Configure prequips.core to use peptideXML.feature ==
 +
 +Return to the Java perspective
 +
 +In the Package Explorer, select prequips.core's prequips.product
 +
 +Select the Configuration tab
 +
 +Select "Remove All" features
 +
 +From the Eclipse IDE Project menu, select "clean all projects" and then "build all"
 +
 +Return to the prequips.product Configuration tab
 +
 +Select "Add" feature
 +
 +Select peptideXML.feature then "OK"
 +
 +Select the "Overview" tab of prequips.product
 +
 +Under the section titled "Testing", select Synchronize
 +
 +== To check out prequips.feature ==
 +
 +Open the SVN repository perspective again
 +(Window -> Open Perspective -> Other -> SVN Repository Exploring)
 +
 +Right click on prequips.feature
 +
 +Select Checkout
 +
 +Select "Check out as a project in the workspace"
 +
 +[NLK: think this might need to be checked out similarly to peptideXML.feature
 +checkout - as a New Feature Project...]
 +
 +Select Finish
 +
 +== Lauch prequips_core ==
 +
 +Right click on prequips_core
 +
 +Select "Run As" and then "Run" to get the launch configuration menu
 +
 +Select the Plug-ins tab
 +
 +Under Workspace Plug-ins check the boxes to include any of the features
 +that you checked out and configured
 +(for example, peptideXML plugin)
 +
 +Select "Add Required Plug-ins"
-== Checking Out ==+Select "Run"

Current revision

This page describes how to set up Eclipse to modify or add features of Prequips.

Contents

[edit]

Required Eclipse Features

You will need the following Eclipse features to build and launch Prequips:

  1. Eclipse Project SDK 3.1.2 - 3.2.1 (download from http://www.eclipse.org or a mirror site)
  2. EMF SDK 2.1.2 - 2.2.1(download manually the EMF-SDO-XSD build. The update site is: http://download.eclipse.org/tools/emf/updates/site.xml)
  3. Subclipse to access the Subversion repository (update site: http://subclipse.tigris.org/update/site.xml,

or use latest unstable: http://subclipse.tigris.org/update_1.2.x)

[edit]

Getting the Eclipse Project SDK

Go to http://www.eclipse.org/downloads/index_project.php and select Platform under Eclipse Project. On the next page select build (tested for 3.1.2 - 3.2.1).

Download the archive and extract it into a directory of your choice. Your Eclipse installation can live within that directory and there's no need to have administrator privileges to set up the software.

[edit]

Installing Features From Within Eclipse

Once you have downloaded and set up the Eclipse Project SDK you can use the Eclipse Update Manager to add the other features. Simply go to Help > Software Updates > Find and Install .... Select Search for new features to install and then select New Remote Site .... Enter a name and the corresponding update site URLs. Then select the latest version of the feature and install. (NOTE, that had to install EMF manually to get the version that also contained XSD)

[edit]

Subversion Repository

Prequips source code can be retrieved from the Subversion repository located at http://db.systemsbiology.net/svn/ngehlenb. To browse the repository comfortably use http://db.systemsbiology.net/cgi-bin/ngehlenb-cgi/viewcvs/viewcvs.cgi.

Access: The repository is no longer world-accessible. If you want to read from or write to the repository please contact Nils Gehlenborg.

[edit]

Checking Out the Main Application

After you have installed the Subclipse plug-in go to Window > Open Perspective > Other ... and select SVN Repository Exploring. Right-click in the SVN Repository tab and go to New > Repository Location .... Enter the repository location shown in the previous section and click Finish.

A list of projects will show up in the view. Select the prequips_core project and right-click it. Select Checkout ... and then Check out as project configured using the New Project Wizard. Don't select the other option, it will get you into trouble when you try to build the project.

Click on Finish and then select Plug-in Project under Plug-in Development in the New Project Wizard. Enter prequips_core or something similar as project name and click Next. On the next page click Finish. All project settings will be imported from the repository. There is no need to enter anything.

[edit]

Checking Out the prequips_external

prequips_external holds 3rd party libraries such as log4j and xerces. These libraries are needed by MSXMLParser

Open the SVN repository perspective again (Window -> Open Perspective -> Other -> SVN Repository Exploring)

Right click on prequips_external

Select Checkout

Select "Check out as a project in the workspace"

Select Finish

[edit]

Add prequips_external to Java Build Path Libraries

Open the Java perspective (Window -> Open Perspective -> Java)

Right click on prequips_core

Select Build Path --> Configure Build Path

Select the "Libraries" tab in the new window

Select "Add Class folder"

Check prequips_external and then select "Okay"


[edit]

Check out peptideXML and peptideXML.feature

Open the SVN repository perspective (Window -> Open Perspective -> Other -> SVN Repository Exploring)

Right click on peptideXML

Select "Checkout as a project configured using the New Project Wizard", then "finish"

Select "Plugin Project" from the New Project Wizard panel

Use "peptideXML" as the project name, then "Next", then "Finish"

In the SVN repository perspective, right click on peptideXML.feature

Select "Checkout as a project configured using the New Project Wizard"

In the New Project Wizard panel, open the Plug-in development folder, and select "Feature Project"

Enter peptideXML.feature as the Project Name and select "Finish"

[edit]

Configure prequips.core to use peptideXML.feature

Return to the Java perspective

In the Package Explorer, select prequips.core's prequips.product

Select the Configuration tab

Select "Remove All" features

From the Eclipse IDE Project menu, select "clean all projects" and then "build all"

Return to the prequips.product Configuration tab

Select "Add" feature

Select peptideXML.feature then "OK"

Select the "Overview" tab of prequips.product

Under the section titled "Testing", select Synchronize

[edit]

To check out prequips.feature

Open the SVN repository perspective again (Window -> Open Perspective -> Other -> SVN Repository Exploring)

Right click on prequips.feature

Select Checkout

Select "Check out as a project in the workspace"

[NLK: think this might need to be checked out similarly to peptideXML.feature checkout - as a New Feature Project...]

Select Finish

[edit]

Lauch prequips_core

Right click on prequips_core

Select "Run As" and then "Run" to get the launch configuration menu

Select the Plug-ins tab

Under Workspace Plug-ins check the boxes to include any of the features that you checked out and configured (for example, peptideXML plugin)

Select "Add Required Plug-ins"

Select "Run"

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Prequips:Eclipse_Setup"
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