Local Installation of Strap
Local installation is more robust than Java Webstart.
The essential file is strap.jar (2.3 MByte) which can be started with the command java -jar strap.jar or by double click.
A small helper file strap.bat (Windows), strap.command (Mac) or strap.sh (Linux)
moves the jar file to the Strap folder $HOME/.StrapAlign/. It identifies existing Java installations.
If needed, it will download and install Java for Windows, Mac or Linux on x86 platforms (50 to 80 MByte).
For downloading Java, the script has the capability to detect web proxies.
Finally it will start strap.jar.
The same script file is used for installation and for running.
Any Web-proxy will be automatically identified within Strap.
Start Strap either
- from the desktop or the Downloads folder by double click or right-click Open ...
or from the command prompt:
- Protein or alignment files can be given as program parameters. In this case the user should change into the project directory before starting Strap.
- Wild cards under Mac, Unix and Linux
- Command line options -D... or -X... or JVM_... are passed to the Java Virtual Machine. For example -Xmx500M would set the memory to 500 MByte.
Download the file
The zip file contains strap.bat
It can simply be dragged to the desktop.
by double click.
The file strap.jar
will be moved to %HOMEPATH%\.StrapAlign\
At Windows command prompt, parameters containing equals sign, space or semicolon need to be quoted.
For Windows XP only: If Java should be installed automatically, then extract bitsadmin.exe to the same directory bitsadmin.zip
Method 1 Users who are familiar with the command terminal can download and run Strap with the following lines using copy-and-paste.
mkdir -p ~/.StrapAlign
wget -O ~/.StrapAlign/strap.sh http://www.bioinformatics.org/strap/install2/strap.sh?$(date +%s)
wget -O ~/.StrapAlign/strap.jar http://www.bioinformatics.org/strap/strap.jar?$(date +%s)
After installation, Strap can also be started from the command prompt with ~/.StrapAlign/strap.sh or by clicking the file ~/Desktop/Strap.desktop.
Under Linux, a menu item will be installed in the application menu.
Method 2 Strap can be installed by downloading
The files strap.sh, strap.jar and install_strap.desktop inside the zip archive need to be extracted.
Double click or right click install_strap.desktop or strap.sh.
Details: The bash file strap.sh is used to install and to run Strap.
It will copy itself to ~/.StrapAlign/.
During installation, the file strap.jar resides in the same parent folder as strap.sh and will be moved by the script to ~/.StrapAlign/.
For security reasons, the ability to launch executable files by double click has been dropped for security reasons in Gnome.
As a workaround, the file install_strap.desktop can be double clicked which in turn will start strap.sh.
Download the zip archive containing Strap.app (2.3 MByte).
Move Strap.app to the Desktop or the Dock. This step is important since it won't start from inside the zip archive.
Right-click Strap.app and select "Open" from the context menu.
Strap will be started.
Note that double click won't work because it is not signed.
When Strap.app is started, the file
is run in /bin/bash.
The files inside Strap.app
can be inspected with the menu item "Show contents" in the context menu (Right-click).
The file Contents/MacOS/strap.jar
is moved to
Inside the Terminal-App Strap can also be installed in the following way:
mkdir -p ~/.StrapAlign
curl -o ~/.StrapAlign/strap.command http://www.bioinformatics.org/strap/install2/strap.sh?$(date +%s)
curl -o ~/.StrapAlign/strap.jar http://www.bioinformatics.org/strap/strap.jar?$(date +%s)
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"
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.
Jar-files are zip archives. The source code is contained in strap.jar and can be compiled with javac.
However, it has passed a preprocessing step making it hard to read.
The original source code is available here: