◦ LONI: http://pipeline.loni.ucla.edu
◦ NITRC: http://www.nitrc.org/projects/pipeline
◦ BIRN: http://www.birncommunity.org/tools-catalog/loni-pipeline
◦ Bioinformatics.org: http://www.bioinformatics.org/pipeline
◦ Try the LONI Pipeline Informatics and Genomics Workflows online without any software installation using anonymous guest account: http://pipeline.loni.ucla.edu/PWS
Operating system(s): Pipeline clients and servers are platform-independent, while some features (e.g. privilege escalation, failover) require the server run on Linux/UNIX OS. The Distributed Pipeline Server (DPS) graphical user interface, which installs the Pipeline server, Grid Engine, and computational imaging and informatics software tools, require standard Linux OS kernels. The Pipeline Web Start (PWS) allows users to start the Pipeline application directly from the web browser and run it locally without any installation. It has all the features and functionality of the downloadable stand-alone Pipeline application and allows anonymous guest access or user-authentication to connect to remote Pipeline servers.
Programming language: Pure Java.
◦ Requirements Summary: The Pipeline client and server can run on any system that is supported by Java Runtime Environment (JRE) 1.5 or higher. Windows Pipeline servers will not be able to use privilege escalation. Three-tier Failover feature is only supported by Unix/Linux systems. All other features are available for all platforms. Most Distributed Pipeline Servers require 300-1,000MB memory, which may depend on the load and garbage collection preferences.
◦ For distributed multicore deployment, the Distributed Pipeline Server (DPS) requires a Grid manager (e.g., Distributed Resource Management Application API, DRMAA), which is provided with the DPS distribution. The Pipeline server will still work on a platform without a Grid manager, however, jobs may not be processed in parallel and performance on multicore machines may be suboptimal.
◦ Complete requirements:
▪ Client: http://pipeline.loni.ucla.edu/support/user-guide/installation/
▪ Server: http://pipeline.loni.ucla.edu/support/server-guide/installation/
▪ DPS: http://pipeline.loni.ucla.edu/DPS
▪ PWS: http://pipeline.loni.ucla.edu/PWS
◦ Each new informatics tool which needs to be accessible as a processing module within the Pipeline environment needs to be described manually by an expert using the Pipeline GUI or automatically using a properly configured XML exporter (e.g., http://www.loni.ucla.edu/twiki/bin/view/MAST/TranslateTo). Then the Pipeline XML module description can be shared with other users.
◦ To run available Pipeline workflows (*.pipe workflow files) on remote Pipeline-servers, users need to have accounts on the remote Pipeline servers. In addition, 2 types of updates may be necessary in the PIPE files - the server-name references of data sources (inputs), data sinks (results), and executables, as well as the path references to the data sources, sinks and executables. The server-name can be easily updated using server changer tool in Pipeline (Tools menu → Server Changer). User has to edit path references on some or all of the data sources, sinks and executables for their server. No workflow modifications are necessary for executing these pipeline workflows on the LONI Pipeline Cranium server; however this requires a LONI Pipeline user-account http://www.loni.ucla.edu/Collaboration/Pipeline/Pipeline_Application.jsp. A proper administrator configuration of the Distributed Pipeline Server (DPS, http://pipeline.loni.ucla.edu/DPS) will resolve the need for such revisions by the user.
◦ Some computational tools may require wrapper scripts that call the raw executable binaries. These scripts (not the raw binaries) are then invoked via the Pipeline environment. Example situations include tools that have implicit outputs, or if the tools routinely return non-trivial exit codes, distinct from zero. Such problems may cause the Pipeline environment to halt execution of subsequent modules, because of a broken module-to-module communication protocol.
◦ Smartlines, which auto-convert between different informatics data formats, need to be extended to handle informatics and genomics data (currently, smartlines handle mostly image file format conversions).
◦ Access to external informatics databases may need to be customized - e.g., PDB http://www.rcsb.org, SCOP http://scop.mrc-lmb.cam.ac.uk/scop, GenBank http://www.ncbi.nlm.nih.gov/genbank, etc.
◦ Native vs. Virtual Pipeline server: The fully distributed pipeline server (DPS) architecture (which allows anyone to locally download, configure and deploy the complete Pipeline server) provides (natively) both the Pipeline middleware as well as installers for all computational tools available on the LONI Cranium Pipeline Grid Server http://pipeline.loni.ucla.edu/support/user-guide/interface-overview/. The virtual Pipeline server and pipeline clients also provide the complete Pipeline environment for a virtual VMware invocation http://pipeline.loni.ucla.edu/PNVE.