PGP and Tranche

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Tranche

In order to increase the utility of project data and make more of it available to the public, the Pesonal Genome Project (PGP) has launched PersonalGenomes@Home. This effort uses Tranche for persistent storage. The Tranche Project is a free and open source file sharing tool that enables collections of computers to easily share and cite scientific data sets. Designed and built with scientists and researchers in mind, Tranche essentially solves the data sharing problem in a secure and scalable fashion.

Tranche User Account

To apply for a user account fill out the form at Tranche User Account Application. Pending account applications are reviewed weekly on Mondays.

System Requirements

Java Runtime Environment 5.0 or later; See System Requirements

Tranche User Guide and Instructions for Up- and Downloads

A detailed user guide can be found Tranche User Guide here.

There are three ways to add or get data from the network:

  1. GUI: Go to the Tranche homepage and click "Launch Tranche". (Requires Java 5+ with Web Start)
  2. Command-line tools: See below
  3. Java API: For custom tools development

The most popular of the three is the GUI, as it is easy to use. The command-line tools are useful for automating tasks or working in headless environments, and the API is useful when integrating Tranche in a software project or for creating a custom tool

Tranche up- and downloads can be run over the command line using the upload tool and the download tool. 

wget http://tranche.proteomecommons.org/files/CommandLineAddFileTool.zip  
wget http://tranche.proteomecommons.org/files/CommandLineGetFileTool.zip

In order to use these tools you also need a certificate, which you can get instantly at Tranche Autocert. It comes in the form of USER.zip.encrypted.

Download each tool, unzip the file, go into unzipped directory, type java -jar NAME.jar --help to obtain usage information. (If java is not in your system path, add it to your path or type the full path /path/to/java -jar NAME.jar --help.

For usage information java -jar Tranche-Downloader.jar --help
Download a project with a certain hash: java -jar Tranche-Downloader.jar HASH

For usage information: java -jar Tranche-Uploader.jar --help
Upload a file:
java -Xmx521m -jar Tranche-Uploader.jar -u USER.zip.encrypted -p PASSWORD -c true -t "MY TITLE" -d "MY DESCRIPTION" /home/DataForUpload

There is the option to download/upload encrypted data:
java -jar Tranche-Downloader.jar -e supersecret HASH
java -jar Tranche-Uploader.jar -u FILE.zip.encrypted -p supersecret /home/DataForDownpload

Example scripts are provided: download script and upload script.

To get notified about changes and upgrades one can join the automated tool group for command-line tools and API.


Transferring Data onto Tranche

There are several options to transfer data onto Tranche:

  • using the command line upload tool from any computer
  • ship 1 TB USB drives or internal drives back and forth (This might be the best option. We simply need to ask Andrew at BPF
    Biopolymers Facility
    77 Ave. Louis Pasteur
    Room 0088
    Boston, MA 02115

--AWZ 19:59, 16 December 2008 (EST))

  • directly from tape; depending on format, the Tranche team has some access to a couple of tape drives; this may be slow
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