Pinned Repositories
Documentation
Wiki of CyVerseUK project. Tutorials and overview of technologies.
fastq-dump
GWASSER
Dockerized Agave app for GWASSER, an R script for simple gwassing.
mikado
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
polymarker
Dockerized Agave app for Polymarker, a SNP assay development pipeline
portcullis
portcullis tool by Dan Mapleson - https://github.com/maplesond/portcullis
RAxML
RAxML agave app and docker image
renseq
Renseq Pacbio pipeline
templates
base templates for Dockerfile and wrappers
tuxedo
Tuxedo suite for up to 4 conditions
CyVerse UK's Repositories
cyverseuk/Documentation
Wiki of CyVerseUK project. Tutorials and overview of technologies.
cyverseuk/renseq
Renseq Pacbio pipeline
cyverseuk/polymarker
Dockerized Agave app for Polymarker, a SNP assay development pipeline
cyverseuk/templates
base templates for Dockerfile and wrappers
cyverseuk/ansible_plays
cyverseuk/blast
blast docker image and cyverse integration
cyverseuk/cyverse_website
cyverseuk/cyverseuk-util
A collection of scripts for the cyverse UK clusters
cyverseuk/GWASSER
Dockerized Agave app for GWASSER, an R script for simple gwassing.
cyverseuk/mikado
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
cyverseuk/bedtools
cyverseuk/Bowtie2
cyverseuk/btrim
cyverseuk/concatenate_files
cyverseuk/Cufflinks
cyverseuk/cut_columns
cyverseuk/cutadapt
cyverseuk/cyverseone
OpenNebula web api to instantiate services from CyVerse UK infrastructure
cyverseuk/emblebi-ena-submit
Docker build to submit to the EMBL-EBI ENA
cyverseuk/kallisto
cyverseuk/MUSCLE
cyverseuk/NCBI_SRA_import
cyverseuk/ocsi
cyverseuk/ontologizer
cyverseuk/Retrieve_BIP_Phenotypes
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.
cyverseuk/samtools
cyverseuk/sickle
cyverseuk/Tophat2
cyverseuk/Trimmomatic
docker image and Agave app for Trimmomatic software
cyverseuk/uncompress_gunzip