Method 1 Users who are familiar with the command terminal can download and run Strap with the following lines using copy-and-paste.

          mkdir -p ~/.StrapAlign
          wget -O ~/.StrapAlign/strap.sh  http://www.bioinformatics.org/strap/install2/strap.sh?$(date +%s)
          wget -O ~/.StrapAlign/strap.jar http://www.bioinformatics.org/strap/strap.jar?$(date +%s)
          bash ~/.StrapAlign/strap.sh
        

After installation, Strap can also be started from the command prompt with ~/.StrapAlign/strap.sh or by clicking the file ~/Desktop/Strap.desktop. Under Linux, a menu item will be installed in the application menu.

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Method 2 Strap can be installed by downloading strap-linux-unix.zip. The files strap.sh, strap.jar and install_strap.desktop inside the zip archive need to be extracted.

Double click or right click install_strap.desktop or strap.sh.

Details: The bash file strap.sh is used to install and to run Strap. It will copy itself to ~/.StrapAlign/. During installation, the file strap.jar resides in the same parent folder as strap.sh and will be moved by the script to ~/.StrapAlign/. For security reasons, the ability to launch executable files by double click has been dropped for security reasons in Gnome. As a workaround, the file install_strap.desktop can be double clicked which in turn will start strap.sh. Download the zip archive containing Strap.app (2.3 MByte).

Move Strap.app to the Desktop or the Dock. This step is important since it won't start from inside the zip archive.

Right-click Strap.app and select "Open" from the context menu. Strap will be started.

Note that double click won't work because it is not signed.

How does it work:

When Strap.app is started, the file Contents/MacOS/strap.command inside Strap.app is run in /bin/bash. The files inside Strap.app can be inspected with the menu item "Show contents" in the context menu (Right-click). The file Contents/MacOS/strap.jar is moved to $HOME/.StrapAlign.

Inside the Terminal-App Strap can also be installed in the following way:

            mkdir -p ~/.StrapAlign
            curl -o ~/.StrapAlign/strap.command http://www.bioinformatics.org/strap/install2/strap.sh?$(date +%s)
            curl -o ~/.StrapAlign/strap.jar http://www.bioinformatics.org/strap/strap.jar?$(date +%s)
            bash ~/.StrapAlign/strap.command
          

Strap will detect Web proxy settings automatically by probing a bunch of web addresses with different settings. It will report success or failure.

If proxy detection fails or to speed up the start of Strap: Assume, the proxy host is proxy.organization.com and the port is 8080. Rename the script file to.

        "PH=proxy.organization.com PP=8080 more text if you like"
      

PH= and PP= must be upper case. The separating spaces are important. There must be no space at the equals sign.

To change settings, edit the script file strap.

• OutOfMemoryError: The parameter in the form -Xmx200M sets the maximum memory limit to 200 MByte. Increase in case of OutOfMemoryError.
• The absolute path to /bin/java.exe.
• Macintosh screen menu bar: Modify the file strap.command with the text editor: Add -Dapple.laf.useScreenMenuBar=true after the Java command.

Strap offers some utilities. They are activated with certain command line parameters.

• Protein/alignment file conversion: Use command line options -toFasta, -toMultipleFasta, -toClustal.
• Strap can be used as a text viewer for very large files with advanced search text highlighting. Use the command line option -textViewer.
• Strap can be used to manage pubmed abstracts and PDF full text. Text pattern highlighting allows text mining by eye in large amounts of pubmed abstracts. Use the command line option -pubmed.