CyVerse UK

All

39 repositories

cyverse_website
Public
website django bioinformatics web-app cyverseuk
Python
•
MIT License
•0•0•0•67•Updated Sep 5, 2024Sep 5, 2024
cyverseone
Public
OpenNebula web api to instantiate services from CyVerse UK infrastructure
0•0•0•0•Updated Sep 7, 2022Sep 7, 2022
Documentation
Public
Wiki of CyVerseUK project. Tutorials and overview of technologies.
docker documentation bioinformatics hpc agaveapi hpc-applications condor tutorial wiki cyverseuk
0•2•0•0•Updated Sep 26, 2019Sep 26, 2019
renseq
Public
Renseq Pacbio pipeline
docker bioinformatics cyverseuk hpc-applications renseq-pacbio-pipeline
Shell
•2•2•0•1•Updated Sep 19, 2019Sep 19, 2019
ansible_plays
Public
docker ansible htcondor condor ansible-playbooks
0•0•0•0•Updated Aug 21, 2019Aug 21, 2019
Cufflinks
Public
dockerfile bioinformatics rna-seq hpc cyverseuk agaveapi hpc-applications cyverse cufflinks
Shell
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MIT License
•0•0•0•0•Updated Mar 7, 2019Mar 7, 2019
templates
Public
base templates for Dockerfile and wrappers
docker template dockerfile wrapper workshop cyverseuk agaveapi
Dockerfile
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MIT License
•0•1•0•0•Updated Oct 5, 2018Oct 5, 2018
kallisto
Public
docker bioinformatics hpc cyverseuk hpc-applications kallisto
Shell
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MIT License
•0•0•0•0•Updated Sep 11, 2018Sep 11, 2018
mikado
Public
Docker image and JSON files for CyverseUK for Mikado, a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies
docker bioinformatics hpc transcripts cyverseuk hpc-applications transcript mikado multiple-transcript-assemblies
Shell
•
MIT License
•0•0•1•0•Updated May 11, 2018May 11, 2018
ocsi
Public
dockerfile application bioinformatics cyverseuk agaveapi cyverse
Python
•1•0•0•0•Updated Apr 10, 2018Apr 10, 2018
blast
Public
blast docker image and cyverse integration
dockerfile bioinformatics hpc cyverseuk hpc-applications nucleotides docker-image blast cyverse
Shell
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MIT License
•0•0•0•0•Updated Feb 13, 2018Feb 13, 2018
polymarker
Public
Dockerized Agave app for Polymarker, a SNP assay development pipeline
docker bioinformatics hpc cyverseuk hpc-applications wheat wheat-genome polymarker snp-assay-development
Shell
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MIT License
•1•1•0•0•Updated Feb 8, 2018Feb 8, 2018
cut_columns
Public
bioinformatics hpc tabular-data columns cyverseuk agaveapi hpc-applications cyverse
Shell
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MIT License
•0•0•0•0•Updated Sep 21, 2017Sep 21, 2017
cyverseuk-util
Public
A collection of scripts for the cyverse UK clusters
ansible documentation ansible-playbook hpc-applications hpc condor
Python
•1•0•0•0•Updated Jul 31, 2017Jul 31, 2017
GWASSER
Public
Dockerized Agave app for GWASSER, an R script for simple gwassing.
docker bioinformatics gwas hpc cyverseuk hpc-applications
R
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GNU General Public License v2.0
•1•0•1•0•Updated Jul 14, 2017Jul 14, 2017
samtools
Public
dockerfile sorting bam-files bioinformatics hpc cyverseuk agaveapi hpc-applications cyverse samtools
Shell
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MIT License
•0•0•0•0•Updated May 24, 2017May 24, 2017
sickle
Public
dockerfile bioinformatics hpc trimming fastq cyverseuk agaveapi hpc-applications cyverse
Shell
•
MIT License
•0•0•0•0•Updated May 24, 2017May 24, 2017
bedtools
Public
dockerfile bioinformatics hpc docker-image cyverseuk hpc-applications bedtools
Shell
•
MIT License
•1•0•0•0•Updated May 22, 2017May 22, 2017
MUSCLE
Public
dockerfile bioinformatics hpc cyverseuk agaveapi hpc-applications sequence-alignment cyverse muscle
Shell
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MIT License
•1•0•0•0•Updated May 16, 2017May 16, 2017
btrim
Public
dockerfile bioinformatics hpc trimming cyverseuk agaveapi hpc-applications cyverse
Shell
•
MIT License
•0•0•0•0•Updated May 16, 2017May 16, 2017
Tophat2
Public
dockerfile bioinformatics tophat cyverseuk agaveapi samtools cyverse bowtie2
Shell
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MIT License
•0•0•0•0•Updated May 16, 2017May 16, 2017
ontologizer
Public
dockerfile bioinformatics hpc ontology gene-ontology cyverseuk agaveapi hpc-applications cyverse
Shell
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MIT License
•0•0•0•0•Updated May 16, 2017May 16, 2017
Bowtie2
Public
dockerfile bioinformatics hpc cyverseuk hpc-applications sequence-alignment cyverse bowtie2
Shell
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MIT License
•0•0•0•0•Updated May 15, 2017May 15, 2017
Trimmomatic
Public
docker image and Agave app for Trimmomatic software
dockerfile bioinformatics hpc trimming cyverseuk agaveapi hpc-applications cyverse docker-image agave
MIT License
•0•0•1•0•Updated May 11, 2017May 11, 2017
cutadapt
Public
dockerfile bioinformatics hpc cyverseuk agaveapi hpc-applications cutadapt
Shell
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MIT License
•0•0•0•0•Updated May 8, 2017May 8, 2017
emblebi-ena-submit
Public
Docker build to submit to the EMBL-EBI ENA
Python
•0•0•0•0•Updated May 5, 2017May 5, 2017
uncompress_gunzip
Public
compression hpc cyverseuk agaveapi hpc-applications cyverse gunzip
MIT License
•0•0•0•0•Updated Apr 21, 2017Apr 21, 2017
concatenate_files
Public
bioinformatics hpc cyverseuk agaveapi concatenation hpc-applications cyverse concatenate-files
Shell
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MIT License
•0•0•0•0•Updated Apr 21, 2017Apr 21, 2017
NCBI_SRA_import
Public
dockerfile bioinformatics aspera ncbi cyverseuk docker-image sra
Shell
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MIT License
•0•0•0•0•Updated Apr 20, 2017Apr 20, 2017
Retrieve_BIP_Phenotypes
Public
Docker container for retrieveing Phenotypic data from the Brassica Information Portal. It uses the BIP-API, stores output in .csv-format and passes the Sequence IDs on into a .txt file for further queries.
docker cyverseuk bip cyverse agave bip-api retrieve-brassica-phenotypes brassica-information-portal
Ruby
•0•0•0•0•Updated Apr 12, 2017Apr 12, 2017