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easybuild-nf

This is an internal pipeline for installing modules/softwares via easy build config files using parallelization of nextflow

https://github.com/arunbodd/easybuild-nf

Science Score: 31.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

This is an internal pipeline for installing modules/softwares via easy build config files using parallelization of nextflow

Basic Info
  • Host: GitHub
  • Owner: arunbodd
  • License: mit
  • Language: Groovy
  • Default Branch: main
  • Size: 173 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License Citation

README.md

!/bin/bash

OBJECTIVE: Learn how to install modules with EasyBuild

DATE: 7/10/2024

AUTHOR: S.Chill

Manual Installations

source the setup

source /apps/x8664/scbs/easybuildsetup.sh

load easybuild

module load EasyBuild

Install your module

eb \ /scicomp/groups-pure/Projects/easybuild/easybuild-easyconfigs/easybuild/easyconfigs///.eb \ --robot \ --detect-loaded-modules=unload \ --accept-eula-for=CUDA

run post installation script

sudo /apps/x8664/scbs/postinstall.sh

verify the module is installed and works

module availe / --help --version

Single Run Installations

NOTES:

Process

check: checks installation status of all modules in given input
single: runs single installations, consecutively
nf: runs nextflow workflow
post: post installation chmod / cleanup

Input

input file with the structure pathOfConfig,Software,Version

outDir

path to outDir

Utilize Run Script

Example: bash run_easybuild.sh

bash runeasybuild.sh run samcompiled/node1.txt sam_compiled/node1

Single Run Installations, no interaction

NOTES:

Process

check: checks installation status of all modules in given input
single: runs single installations, consecutively
nf: runs nextflow workflow
post: post installation chmod / cleanup

Input

input file with the structure pathOfConfig,Software,Version

outDir

path to outDir

Utilize Run Script with nohup

Example: nohup bash run_easybuild.sh > 2>&1 &

nohup bash runeasybuild.sh run conf/critical.csv /scicomp/groups-pure/Projects/easybuild/critical > /scicomp/groups-pure/Projects/easybuild/critical/criticalnohup.txt 2>&1 &

NF Installations, no interaction

NOTES:

Process

check: checks installation status of all modules in given input
single: runs single installations, consecutively
nf: runs nextflow workflow
post: post installation chmod / cleanup

Input

input file with the structure pathOfConfig,Software,Version

outDir

path to outDir

Utilize Run Script with nohup

Example: nohup bash run_easybuild.sh > 2>&1 &

nohup bash runeasybuild.sh nf conf/critical.csv /scicomp/groups-pure/Projects/easybuild/critical > /scicomp/groups-pure/Projects/easybuild/critical/criticalnohup.txt 2>&1 &

Check

NOTES:

Process

check: checks installation status of all modules in given input
single: runs single installations, consecutively
nf: runs nextflow workflow
post: post installation chmod / cleanup

Input

input file with the structure pathOfConfig,Software,Version

outDir

path to outDir

Utilize Run Script

Example: bash run_easybuild.sh

bash run_easybuild.sh check

Post admin modifications

NOTES:

Process

check: checks installation status of all modules in given input
single: runs single installations, consecutively
nf: runs nextflow workflow
post: post installation chmod / cleanup

Input

input file with the structure pathOfConfig,Software,Version

outDir

path to outDir

Utilize Run Script with nohup

Example: bash run_easybuild.sh

bash run_easybuild.sh post

Owner

  • Name: Arun boddapati
  • Login: arunbodd
  • Kind: user
  • Location: Reston
  • Company: Leidos

Citation (CITATIONS.md) 

# cdcgov/easybuild: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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Dependencies

pyproject.toml pypi