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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 Mar 21, 2019 14 issues need help

DataBiosphere / toil

575

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

cwl python mesos slurm gridengine workflow pipeline aws azure common-workflow-language

Python Updated Mar 22, 2019

gc3-uzh-ch / elasticluster

240

Create clusters of VMs on the cloud and configure them with Ansible.

python cluster slurm gridengine hadoop spark ec2 cloud gcp azure clustering hpc ansible

Python Updated Mar 22, 2019 3 issues need help

Azure / batch-shipyard

179

Provision, execute, and monitor batch and HPC container workloads on Azure Batch

azure-batch docker hpc mpi gpu infiniband rdma azure batch-processing nfs glusterfs azure-functions containers singularity windows-containers serverless slurm

Python Updated Mar 13, 2019

PySlurm / pyslurm

116

Python Interface to Slurm

slurm cython python hpc cluster

Python Updated Mar 10, 2019

mllg / batchtools

87

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 Mar 1, 2019 3 issues need help

mschubert / clustermq

61

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 Mar 15, 2019

ohsu-comp-bio / funnel

61

Funnel is a toolkit for distributed task execution via a simple, standard API.

ga4gh google-cloud gridengine slurm pbs-torque docker aws-batch

Go Updated Jan 29, 2019

HenrikBengtsson / future.batchtools

47

🚀 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 Mar 16, 2019

giovtorres / docker-centos7-slurm

37

Slurm Docker Container on CentOS 7

docker slurm centos7 centos hpc

Dockerfile Updated Mar 21, 2019

CSCfi / fgci-ansible

35

🔬 Collection of the Finnish Grid and Cloud Infrastructure Ansible playbooks

ansible ansible-roles slurm grid wlcg cscfi hpc provisioning cluster

Shell Updated Mar 6, 2019 3 issues need help

NERSC / slurm-magic

32

IPython magic for SLURM.

magic-commands slurm jupyter

Python Updated Oct 10, 2018

giovtorres / slurm-docker-cluster

25

A Slurm cluster using docker-compose

hpc slurm slurm-cluster docker-compose

Dockerfile Updated Mar 21, 2019

vpenso / prometheus-slurm-exporter

20

Prometheus exporter for performance metrics from Slurm.

prometheus-exporter slurm

Go Updated Jan 21, 2019

WilsonSayresLab / BioinformaticsIntroduction

20

bioinformatics unix tutorial cluster sftp python lab slurm trainee batch-script

Updated Dec 28, 2018

cryotools / osaris

17

Scripts to facilitate parallel InSAR processing and analysis of Sentinel-1 time series on HPC clusters based on GMTSA…

sar sentinel-1 interferometry slurm high-performance-computing timeseries-analysis

Shell Updated Mar 22, 2019

angt / slurm-https

17

A simple HTTPS API for Slurm

slurm api-server https-server

Go Updated Jan 19, 2016

rokroskar / sparkhpc

15

launching and controlling spark on hpc clusters

hpc-cluster spark python lsf slurm

Python Updated Dec 5, 2018

MikeDacre / fyrd

14

Submit functions and shell scripts to torque and slurm clusters or local machines using python.

torque slurm slurm-cluster bioinformatics-pipeline library python python3 python3-library python2

Python Updated Nov 1, 2018 3 issues need help

psteinb / hpc-in-a-day

13

a temporary fork of softwarecarpentry/hpc-novice

hpc lsf slurm mpi python parallel training

Python Updated Jun 1, 2018

GarrettJenkinson / informME

12

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

jcwright77 / engaging_cluster_howto

11

A brief introduction to the engaging cluster for the NSE and PSFC groups. Assorted recipes and gists.

cluster slurm x2go

Updated Feb 27, 2019

carlochess / uchuva

11

A scientific web portal that allows users to create and submit workflows to HTCondor (Dagman), Slurm, OpenLava (LSF),…

htcondor slurm workflow torque

JavaScript Updated Aug 14, 2017

smdabdoub / phylotoast

11

Tools for phylogenetic data analysis including visualization and cluster-computing support.

python phylogenetics qiime visualization 16s microbiome microbiome-analysis microbial-genomics bioinformatics computational-biology cross-platform hpc pbs slurm

Python Updated Feb 28, 2019

goerz / clusterjob

10

Manage traditional HPC cluster workflows in Python

hpc python slurm

Python Updated Apr 6, 2018

SciDAS / slurm-in-docker

9

Slurm in Docker - Exploring Slurm using CentOS 7 based Docker images

slurm docker rpm-packages centos7 openmpi cluster centos hpc lmod

Shell Updated Nov 11, 2018

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 Mar 16, 2019

HECBioSim / Longbow

9

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

Python Updated Mar 19, 2019

giovtorres / slurmtools

8

Custom Slurm tools

hpc slurm python

Python Updated Nov 4, 2018

chrissamuel / slurm-qog

7

Perl script to generate "quality-of-guess" feedback for users about their requested Slurm walltimes.

slurm hpc gplv2 gpl perl

Perl Updated Jul 15, 2018

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Repositories 162