PGP and Tranche

People

 * User:Andrea Loehr (PGP)
 * User:Alexander Wait Zaranek (PGP)
 * User:James A. Hill (Tranche)
 * User:Bryan E. Smith (Tranche)

Tranche
In order to increase the utility of project data and make more of it available to the public, the Personal Genome Project (PGP) has launched PersonalGenomes@Home. This effort uses ProteomeCommons.org's Tranche Network 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 for a ProteomeCommons User Account. Pending applications are reviewed each business day.

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:   GUI : Go to the Tranche homepage and click "Launch Tranche". (Requires Java 5+ with Web Start)  Command-line tools : See below  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 --no-check-certificate https://proteomecommons.org/tranche/files/CommandLineAddFileTool.zip wget --no-check-certificate https://proteomecommons.org/tranche/files/CommandLineGetFileTool.zip

In order to use these tools you also need a login, which you can get at ProteomeCommons.org.

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</tt>

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 </tt>

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

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.

Download PGP Data from Tranche
The public PGP data are now available on Tranche.

You have two options when downloading using the command-line tool:

1. To download using the project hash and the path information: java -Xmx512m -jar Tranche-Downloader.jar -r 'PATH' PROJECT_HASH

Where PROJECT_HASH is: xz8EIKO6y5dF9yJeH7+71PGu+f/PKjC9TWyg70gcJMDVH/SaUDxgbHrc8O1zBGxDK+cHlSzS5XYc+mk5H8TyVXh9BTYAAAAAAmRoJA==

2. To download using the hash for the individual run ( recommended ):

java -Xmx512m -jar Tranche-Downloader.jar RUN_HASH

Where RUN_HASH can be found in the table below. This second method is recommended because it will likely be faster, as option #2 will not need to load the entire project's information.

The following are available on Tranche. Each of these paths contain directories Cn.1 n=1..36, which each contain the raw images s_lane_tile_[acgt].tif.gz, where the lane is specified in the path by L00lane (e.g. L001), and tile=1..100.