Top 8 singularity Open-Source Projects
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singularity
Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics (by StaPH-B)
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singularity-hpc
Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
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parse-hipaa
HIPAA & GDPR compliant ready parse-server with postgres/mongo, parse-hipaa-dashboard. Compatible with ParseCareKit
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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> It's been a while since you can rerun/resume Nextflow pipelines
Yes, you can resume, but you need your whole upstream DAG to be present. Snakemake can rerun a job when only the dependencies of that job are present, which allows to neatly manage the disk usage, or archive an intermediate state of a project and rerun things from there.
> and yes, you can have dry runs in Nextflow
You have stubs, which really isn't the same thing.
> I have no idea what you're referring to with the 'arbitrary limit of 1000 parallel jobs' though
I was referring to this issue: https://github.com/nextflow-io/nextflow/issues/1871. Except, the discussion doesn't give the issue a full justice. Nextflow spans each job in a separate thread, and when it tries to span 1000+ condor jobs it die with a cryptic error message. The option of -Dnxf.pool.type=sync and -Dnxf.pool.maxThreads=N prevents the ability to resume and attempts to rerun the pipeline.
> As for deleting temporary files, there are features that allow you to do a few things related to that, and other features being implemented.
There are some hacks for this - but nothing I would feel safe to integrate into a production tool. They are implementing something - you're right - and it's been the case for several years now, so we'll see.
Snakemake has all that out of the box.
Singularity is a container platform often used in HPC (high performance computing) because it doesn't require root.
From the git repo: https://github.com/apptainer/apptainer
> Apptainer was formerly known as Singularity and is now a part of the Linux Foundation.
singularity related posts
Index
What are some of the best open-source singularity projects? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | nextflow | 2,557 |
| 2 | singularity | 2,495 |
| 3 | apptainer | 926 |
| 4 | hpc-container-maker | 438 |
| 5 | docker-builds | 169 |
| 6 | singularity-hpc | 106 |
| 7 | parse-hipaa | 94 |
| 8 | shpc-registry | 11 |
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