Pinned Repositories
bcbb
Useful bioinformatics code, primarily in Python and R
cloudbiolinux
CloudBioLinux: automating resource preparation for biological analysis
GenoLogics-LIMS-Python
Python interface to GenoLogics LIMS via its REST API.
gitflow-tests
testing git
scilifelab
Misc code snippets for Science For Life Laboratory
scilifelab_bcbio
irma-scripts
Stand-alone scripts deployed to Irma
miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
ngi_pipeline
Code driving the production pipeline at SciLifeLab
taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
b97pla's Repositories
b97pla/arteria-delivery
Micro-service to carry out deliveries on Uppmax
b97pla/arteria-incubation
Work-in-progress for the upcoming new and improved Arteria packs.
b97pla/arteria-runfolder
A webservice used to monitor runfolders from Illumina instruments and check what state they are in (e.g. ready to process or not).
b97pla/b97pla.github.io
b97pla/charon
Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.
b97pla/checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
b97pla/configs
Config files used to define parameters specific to compute environments at different Institutions
b97pla/docker-notebook
Docker containers for the IPython notebook (+SciPy Stack)
b97pla/hairy-adventure
Base for the automation challenge at SNP&SEQ - let's see which automation system suite our needs best!
b97pla/hercules
b97pla/hugin
Status monitor
b97pla/ipython
Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.
b97pla/irma-provision
Ansible playbooks for provisioning NGI pipeline and related sw
b97pla/irma-scripts
Stand-alone scripts deployed to Irma
b97pla/miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
b97pla/ngi-analysis-manager
b97pla/ngi_pipeline
Code driving the production pipeline at SciLifeLab
b97pla/ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
b97pla/ngi_stats
Gather and plot statistics for NGI sequencing
b97pla/piper
A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper
b97pla/recruitment
b97pla/seqreports
This is a Nextflow pipeline for generating sequencing reports for the SNP&Seq Technology platform, NGI Uppsala, SciLifelab Genomics.
b97pla/sisyphus
Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data
b97pla/snpseq-archive-upload
Rest service for handling archive uploads
b97pla/snpseq-archive-verify
REST service for verifying uploaded archives
b97pla/snpseq_metadata
b97pla/snpseq_packs
StackStorm packs to automate sequencing center operations
b97pla/TACA
Tool for the Automation of Cleanup and Analyses
b97pla/taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
b97pla/track_runfolders
Some tools for tracking the status of runfolders