Search Results for "pbs-drmaa"
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Showing 41 open source projects for "pbs-drmaa"
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1
ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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The Community Scheduler Framework (CSF) is a set of Grid Services, implemented using the Globus Toolkit, which provides an environment for the development of metaschedulers that can dispatch jobs to resource managers such as LSF, SGE, PBS and Condor.
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package-build-service
Tools for building packages in clean chroot environment
Package Build Service (pbs) - Tools for building packages in clean chroot environment: aum++: Tool for building packages in clean chroot environment mass_rebuild: Tool for automatic rebuilding package(s) repo-hdlistgen: Tool for work with own repo genchroot-tarball: Tool for generation chroot archive mass_rebuild_test: Tool for testing installation packages after mass_rebuild pbs: Service for building packages in clean chroot environment (temporary... -
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DRMAA for Torque/PBS Pro library is an implementation of OGF DRMAA 1.0 (Distributed Resource Management Application API) specification for the submission of jobs to Torque and PBS Professional systems. More: http://apps.man.poznan.pl/trac/pbs-drmaa
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
.... A presence/absence matrix is also generated to allow you to identify the core/accessory genome content across all your genomes. The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses. SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available. For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx -
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<myJAM/> is a web based monitoring and accounting tool for HPC clusters with pbs-like batch-systems (e.g. Torque or PBSPro).
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ANTS on CONDOR
Using buildtemplateparallel.sh from ANTS on Condor
... in ANTS's script "buildtemplateparallel.sh" for SGE, PBS and Apple XGrid, but not for Condor yet. This modification enables running buildtemplateparallel.sh from ANTS-1.9.v4 on HTCondor (http://research.cs.wisc.edu/htcondor/) environment. -
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PolySim
Polymer simulation utilites
... to visualize with pymol. For specific non-pdb input/output of 2nd program there are convertation utils also available. Programs are expected to compile in gcc under cygwin or pure linux environment. Scripts to run many copies of program under pbs/torque cluster system are also available. -
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FBSAT
An efficient analysis pipeline for family-based sequencing
Through our tool a user can perform the whole analysis parallelized on UNIX HPC systems controlled by SGE or PBS automatically. Non-bioinformatics researchers can easily and quickly identify variants that are potentially causing diseases while minimizing false positives and artifacts. -
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q pipeline manager
q: integrated platform for pipeline configuration and management
The q utility is a platform for creating and managing data analysis pipelines. It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently... -
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Opal is a toolkit for wrapping scientific applications as Web services on Cluster, Grid and Cloud resources with ease. Users may access these software as a service using simple Web service APIs from their custom application and workflow environment.
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Ganglia Job Monarch
Batch system monitoring and archiving
Job Monarch is an addon to the Ganglia Monitoring System that provides batch job monitoring and archiving plus a graphical overview of clusters and assorted batch systems. Fully supported batch system: Torque, PBS and SLURM. Experimental: LSF, SGE -
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PBS Cluster Viz is a project to display information useful to admins and users about a computing cluster managed by a PBS-compatible resource manager. Information includes load and job distribution. Interactive as well as static output is available.
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Mpaxs
Transparent Local and Remote Parallelization for Java
Mpaxs provides a simple abstraction for executing Callables and Runnables either locally within the same Virtual Machine, on the same host via RMI, or on remote machines, also via RMI. It supports launching of new compute hosts via an extensible API, currently featuring local compute host launching and grid compute host launching using the DRMAA API. -
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parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A patch...
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A simple lightweight system for genomic annotation written in Java. SHAP uses the Spring application framework, Hibernate for persistence and full-text searching of results and DRMAA for Grid computing.
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RNA CoMPASS
RNA CoMPASS is a web-based GUI distributed computational pipeline.
RNA CoMPASS, a web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. RNA CoMPASS is deployable on either a local cluster or a grid environment managed by PBS submission. -
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Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
... are submitted to the cluster depending on attributes set up in the configuration file. Program options can be modified in the main script "DressUp", and PBS options can be modified from the HeaderFiles directory. -
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DCI Bridge is a web application (sevice) that provides standard access to the distributed computing infrastructures (DCIs) like grids, desktop grids, clusters, clouds and service based computational resources by implementing the specification of the OGSA Basic Execution Service 1.0. The DCI Bridge web application creates a transparent layer between the users (workflow systems) and the DCI systems. The user can submit jobs to the various DCI systems using the OGSA Basic Execution Service...
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A set of Java-tools to get Taverna to "play-nice" with a cluster that runs PBS. Please see the homepage link for more details.
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Cross platform GUI managing bookmarks and shortcuts in a portable way. Support import/export, search, encryption, hierarchical tags, USB key installation, various environments integration, OS-dependent shortcuts, plugins extensibility.
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PBS Job Seer is a program which analyses the state of a PBS/Maui batch system and automatically generates a batch script for MPI jobs which would then be able to start immediately.
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A C/C++ based client and server implementation of the OGSA Basic Execution Service, used to provide a Web Services interface to distributed resource managers such as Platform LSF and PBS/PBS Pro. The SOAP stack is provided by the gSOAP toolkit.
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Rapid development of portal-based user interfaces for submitting compute jobs to remote compute resources. It supports the mainstream compute engine vendors Sun Grid Engine, PBS and Condor. Get a job-submission portal up and running in a few hours.
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A web-based monitor for PBS-based clusters (e.g. OpenPBS and Torque). It provides an overview of node usage, running jobs, and active users. It is built on the pbs-python libraries.