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nextflow-io / nextflow

A DSL for data-driven computational pipelines

bioinformatics workflow-engine pipeline pipeline-framework nextflow cloud data-flow groovy sge slurm aws docker singularity hpc singularity-containers reproducible-science reproducible-research

Groovy Updated Oct 20, 2018 19 issues need help

mllg / batchtools

80

Tools for computation on batch systems

cran batchjobs batchexperiments slurm lsf sge docker-swarm torque openlava parallel-computing r high-performance-computing reproducibility hpc hpc-clusters

R Updated Oct 17, 2018 2 issues need help

mschubert / clustermq

54

R package to send function calls as jobs on LSF, SGE, Slurm, PBS/Torque, or each via SSH

high-performance-computing cluster r-package slurm sge lsf ssh

R Updated Oct 5, 2018

HenrikBengtsson / future.batchtools

42

🚀 R package future.batchtools: A Future API for Parallel and Distributed Processing using batchtools

r package hpc parallel distributed-computing torque slurm sge job-scheduler pbs

R Updated Aug 12, 2018

Ensembl / ensembl-hive

30

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource

ensembl workflow-management-system perl java python mysql sqlite postgresql high-performance-computing lsf sge htcondor pbs-pro pipeline farm pbspro ehive docker docker-swarm

Perl Updated Oct 18, 2018

datasnakes / OrthoEvolution

18

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes.

Python Updated Sep 29, 2018

GarrettJenkinson / informME

11

An information-theoretic pipeline for methylation analysis of WGBS data

bioinformatics methylation matlab cpp bash r next-generation-sequencing ising-model information-theory sge parameter-estimation parallel-computing slurm

Matlab Updated Jun 21, 2018 1 issue needs help

HenrikBengtsson / future.BatchJobs

9

🚀 R package: future.BatchJobs: A Future API for Parallel and Distributed Processing using BatchJobs

r package hpc parallel distributed-computing parallel-computing torque job-scheduler slurm pbs sge

R Updated Jul 18, 2018

HECBioSim / Longbow

8

Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an …

Python Updated Sep 28, 2018

zengxiaofei / PJM

5

A simple job manager for PBS (Portable Batch System)

torque pbs bioinformatics-pipeline sge

Python Updated Sep 14, 2017

indigo-dc / bdocker

4

Execution and management of Docker containers in batch systems.

batch-systems sge docker docker-container daemon

Python Updated May 31, 2017

FlyPythons / DAGflow

3

Module to create DAG Task and Manage Task on SGE

sge python pipeline-framework workflow

Python Updated Mar 16, 2018

datasnakes / htseq-count-cluster

3

A cli for running multiple qsub jobs with HTSeq's htseq-count on a cluster.

htseq htseq-count-cluster cluster sge htseq-count rnaseq cli

Python Updated Sep 30, 2018 1 issue needs help

UCL / GERun

2

A wrapper for the various MPI implementations on Legion to abstract them so that users don't need to know all the opt…

mpi legion grace thomas mpirun wrapper sge son-of-grid-engine

Shell Updated May 15, 2018

datasnakes / qsubmitter

2

An R package to submit arbitrary jobs to a remote SGE cluster

qsub sge r

Forked from zachary-foster/qsubmitter R Updated Jun 5, 2018

zenotech / MyCluster

2

Utilities to support interacting with multiple HPC clusters

python2 python scrutinizer multiple-hpc-clusters mycluster slurm quality sge gridengine lsf pbs-torque hpc-cluster hpc

Python Updated Oct 13, 2018 2 issues need help

jrhawley / Terminal

2

Custom terminal setup for Linux and Mac

terminal bashrc-configs bash-alias vimrc tmux-conf sge linux anaconda keyboard

Shell Updated Sep 14, 2018

TheRoddyWMS / BatchEuphoria

2

A library to access different kinds of cluster backends

job-scheduler pbs batch cluster lsf sge roddy

Groovy Updated Aug 21, 2018

CarragherLab / cptools2

2

Running cellprofiler on eddie3 / SGE clusters

cellprofiler python sge biology imaging-informatics hpc-cluster

Python Updated Oct 2, 2018

zengxiaofei / SGE-scripts

1

Some scripts for managing nodes and jobs on SGE

sge cluster-management grid-engine

Forked from FrasergenBioinformatics/SGE-scripts Python Updated Aug 14, 2018

Ensembl / ensembl-hive-sge

1

SGE Meadow for Ensembl Hive

ehive sge perl docker ensembl

Perl Updated Aug 20, 2018

stevekm / docker-centos6-sge

Docker container with CentOS6 & SGE installed

dockerfile docker centos6 sge

Shell Updated Dec 12, 2017

paultsw / mnist_mpi

Proof-of-concept, MPI-based distributed training of a neural network on SGE HPCs.

distributed pytorch mpi sge hpc

Python Updated Aug 6, 2018

eachanjohnson / workflows

Pipeline construction and execution in R

pipeline distributed-computing sge parallel multicore

R Updated Sep 9, 2018

fieldtrip / qsub

This repository contains a subset of the FieldTrip code related to distributed computing

matlab distributed-computing torque slurm sge parallel-computing

Matlab Updated Aug 26, 2018

stevekm / docker-sge

Dockerfile to build a container with SGE installed

docker dockerfile sge container

Forked from gawbul/docker-sge Shell Updated Dec 8, 2017

CarragherLab / scissorhands

Generate eddie3 submission scripts in python

sge cluster-computing python

Python Updated Sep 30, 2018

IBIC / rmake

Running make on an SGE

sge grid-engine makefile make

Shell Updated Dec 7, 2017

efcaguab / sge-workshop

Basic tutorial on the use of the HPC Abacus at the School of Biological Sciences, University of Canterbury

high-performance-computing sge computational-biology

R Updated Apr 16, 2018

zy4 / scala-sge-utils

scala utils for the sun grid engine

sge utility-library scala immutable

Scala Updated Apr 27, 2017

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Repositories 30