jmchilton / swift

Swift user interface to run multiple proteomics search engines + scaffold

Swift

Search multiple tandem mass spec. datafiles using multiple search engines at once: Mascot, Sequest, X!Tandem, OMSSA and Myrimatch.

Swift inputs

Swift accepts one or many raw or mgf files. You can process separate files or entire directories.

Swift outputs

Swift produces Scaffold 3 reports (.sf3 files). You can view these reports on your own computer, just download and install the free Scaffold 3 viewer. There are several possibilities how to map input files to Scaffold reports.

Build

To build Swift, the following is required:

• Java Development Kit 6 ( http://www.oracle.com/technetwork/java/javasebusiness/downloads/java-archive-downloads-javase6-419409.html#jdk-6u27-oth-JPR )
• Maven 3.0.3 ( http://maven.apache.org/download.html )
• git (optional) to obtain the source

Once you have Java and Maven setup, you can build Swift as follows:

Get Swift from github

git clone git://github.com/romanzenka/swift.git

Create swift-3.0-install.zip

cd swift
mvn package -DskipTests
cd target
ls
# You should see swift-3.0-install.zip

• If you want to run all the unit tests, feel free to omit the -DskipTests clause!

Congratulations!

You are ready to install Swift.

• Copy the target/swift-3.0-install.zip to your target machine.
• Unzip it
• Install instructions are in swift-3.0/INSTALL.txt

Please mail [email protected] if you have any problems!