raymond301 / 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, Comet, X!Tandem, and MyriMatch.

Swift inputs

Swift accepts one or multiple raw, mgf, mzML or Agilent .d 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 (or 7) ( http://www.oracle.com/technetwork/java/javasebusiness/downloads/java-archive-downloads-javase6-419409.html#jdk-6u27-oth-JPR )
• Maven 3.0.3 or newer ( 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-$VER-install.tar.gz

cd swift
mvn install -DskipTests
cd swift/installer/target
ls
# You should see swift-$VER-install.tar.gz

• 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 swift/installer/target/swift-$VER-install.tar.gz to your target machine.
• Unzip it
• Install instructions are in swift-$VER/INSTALL.txt

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