PGP and Tranche: Difference between revisions
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==Tranche== | ==Tranche== | ||
In order to run a full analysis of all [http://personalgenomes.org Pesonal Genome Project] (PGP) data and create a distributed computing effort [[PersonalGenomes@Home]], we will collaborate with [http://tranche.proteomecommons.org/about/ Tranche]. 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. | |||
The | |||
====Tranche User Account==== | ====Tranche User Account==== | ||
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==== System Requirements==== | ==== System Requirements==== | ||
Java Runtime Environment 5.0 or later | Java Runtime Environment 5.0 or later; See [http://tranche.proteomecommons.org/users/system-requirements.html System Requirements] | ||
[http://tranche.proteomecommons.org/users/system-requirements.html System Requirements] | |||
====Tranche User Guide and Instructions for Up- and Downloads==== | ====Tranche User Guide and Instructions for Up- and Downloads==== | ||
A detailed user guide can be found | A detailed user guide can be found [http://tranche.proteomecommons.org/users/ Tranche User Guide here]. | ||
Tranche up- and downloads can be run over the command line using the [http://tranche.proteomecommons.org/files/CommandLineAddFileTool.zip upload tool] and the [http://tranche.proteomecommons.org/files/CommandLineGetFileTool.zip download tool]. | Tranche up- and downloads can be run over the command line using the [http://tranche.proteomecommons.org/files/CommandLineAddFileTool.zip upload tool] and the [http://tranche.proteomecommons.org/files/CommandLineGetFileTool.zip 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 [http://www.proteomecommons.org/autocert/ Tranche Autocert]. It comes in the form of USER.zip.encrypted. <br /> | In order to use these tools you also need a certificate, which you can get instantly at [http://www.proteomecommons.org/autocert/ Tranche Autocert]. It comes in the form of USER.zip.encrypted. <br /> | ||
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====Transferring Data onto Tranche==== | ====Transferring Data onto Tranche==== | ||
There are several options to transfer 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 [http://genome.med.harvard.edu/ BPF] --[[User:Alexander Wait Zaranek|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 | |||
Revision as of 17:59, 16 December 2008
People
Tranche
In order to run a full analysis of all Pesonal Genome Project (PGP) data and create a distributed computing effort PersonalGenomes@Home, we will collaborate with Tranche. 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. 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 --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
