Johan Dahlberg

Login: johandahlberg

Company: SNP&SEQ Platform @ Uppsala University

Location: Uppsala

Bio: null

Blog: http://uppsala-bioinformatics.se/

Blog: http://uppsala-bioinformatics.se/

Member of

1. National Genomics Infrastructure
2. Science For Life Laboratory
3. Uppsala University, Department of Medical Sciences, Molecular Medicine

Repositories

algebird

Abstract Algebra for Scala

ansible-elk

Ansible role for Elasticsearch ELK Stack

ansible_spark_openstack

Instructions and Ansible playbooks for deploying a Spark stand-alone cluster on OpenStack

ansible-st2

Ansible playbooks to deploy StackStorm

arteria-bcl2fastq

Provides a simple http-interface for Illumina bcl2fastq

arteria-checksum

Service for checking md5sums

arteria-core

The arteria python module is a library of helper classes for the Arteria project.

arteria-delivery

Micro-service to carry out deliveries on Uppmax

arteria-incubation

Work-in-progress for the upcoming new and improved Arteria packs.

arteria-lib

Contains the arteria core python library as well as smaller services.

arteria-packs

StackStorm packs to automate sequencing center operations

arteria-project.github.io

The Arteria project organization page: http://arteria-project.github.io

arteria-provisioning

Provisioning for the Arteria project

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).

arteria-siswrap

Wraps scripts from Sisyphus (https://github.com/Molmed/sisyphus) with a http-interface.

awesome-10x-genomics

List of tools and resources related to the 10x genomics GEMCode/Chromium system

awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

awesome-public-datasets

An awesome list of high-quality open datasets in public domains (on-going).

bakka

akka + bams = bakka

BestPracticeSlides

Repo for the code used in the MolMed TechTalk about best practices in scientific computing.

checkQC

checkQC inspects the content of a runfolder and determines if it passes a set of quality criteria

clarity-ext

Extensions for Clarity

contAdamination

Hacking away on bloom filters and adam...

courses

Course homepages for some of the courses given at SciLifeLab

curiouscrows

Team repository for the Curious Crows for Hack4Sweden 2016

cwltool

Common Workflow Language reference implementation

ExportR

Project statistics export utility

ExternalProcessExperiment

null

gatk

GATK Official Release Repository

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gatk_sbt_example

An example of how to use GATK Queue with sbt

genomeresources

List of resource file used at the NGI platform

gyllenehjortentrivia

Ett litet webspel om Gyllene Hjorten trivia

hairy-adventure

Base for the automation challenge at SNP&SEQ - let's see which automation system suite our needs best!

HelloGoogleMaps

Some prototyping for a google maps based andoid app.

hercules

null

hungry_aardvarks

A IBM Watson based podcast annotation app prototype

jvar

jvar repo forked from https://code.google.com/p/jvarkit/

jvarkit

Java utilities for NGS

localq

null

ngi_pipeline

Code driving the production pipeline at SciLifeLab (not yet in production)

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

pipeline-provision

Ansible playbooks for provisioning NGI pipeline and Piper

piper

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)

PiperWorkshop

null

public-apis

A collective list of public JSON APIs for use in web development.

relaxbox

Simple slack chatbot to remind you to meditate and record tension levels before and after meditation

role_hercules

Public Ansible role for deploying Hercules

sciluigi

Scientific Luigi

Scripts

My collection of (mostly) bioinformatics related scripts

SDashboard

A visualization app written in Shiny to show sequencing metrics

sisyphus

Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data

snpseq-archive-upload

Rest service for handling archive uploads

SnpSeqPipeline

Variant calling pipeline for the SNP&SEQ Technology Platform at Uppsala University

Splitter

Scala program for splitting files of some common bioinformatics formats (right now fastq.gz and bam)

st2

StackStorm (aka "IFTTT for Ops") is event-driven automation commonly used for auto-remediation, security responses, facilitated troubleshooting, complex deployments, and more. Includes rules engine, workflow,1800+ integrations (see /st2contrib), native ChatOps and so forth. Installer available at http://docs.stackstorm.com/install/index.html. Ping us on slack - https://stackstorm-community.slack.com/.

st2workroom

Vagrant environment used to play with StackStorm, develop StackStorm for your environment, or develop on StackStorm itself!

swingbeats

A little web app to get swing dance music playlists from spotify.

taca-ngi-pipeline

A TACA plugin adding functionality relevant for the ngi_pipeline

tattoo

A show of Pipers - or a prototype for a project management system

uppsala-bioinformatics.se

My personal website

vagrant-puppet-slurm

A playground for testing setting up a slurm cluster (for testing purposes only).

valdata

Analysis of voting patterns in the Swedish general election 2014.

virtualbox-cluster

A (currently only 3 node) virtualbox cluster for quickly testing out things

workflows

Community maintained workflows & tools (with examples)

Commits To