John Chilton

Login: jmchilton

Company: Penn State University

Location: State College, PA

Bio: Research software developer for @galaxyproject and co-founder of @common-workflow-language. I turn McDonald's hash browns into pull requests.

Blog: http://twitter.com/jmchilton

Blog: http://twitter.com/jmchilton

Member of

1. Galaxy Project

Repositories

2015-bosc

Abstract and presentation material for the Biometrics Open Source Conference 2015

aliased_sql

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ansible-galaxy

An Ansible role for managing a Galaxy (http://galaxyproject.org) server.

ansible-galaxy-extras

Extra stuff to help bootstrap a Galaxy server.

ansible-galaxy-os

An Ansible role is for configuring the base operating system useful for running Galaxy.

ansible-galaxy-toolshed

An Ansible role for managing a Galaxy (http://galaxyproject.org) Tool Shed server. For a role to install Galaxy itself, see https://github.com/galaxyproject/ansible-galaxy

auto-mulled

Generating Docker containers from bioconda on the fly with Travis cron-job feature.

bamtools

Collection of Galaxy wrappers for Bamtools

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

bdbag

Big Data Bag Utilities

bioblend

A python library for interacting with CloudMan and Galaxy API

bioblend-tutorial

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biocloudcentral

Easily launch CloudMan and CloudBioLinux clusters with no manual configuration

biocloudcentral-puppet

Puppet Config for Deploying biocloudcenral (https://github.com/chapmanb/biocloudcentral)

bioconda-recipes

Conda recipes for the bioconda channel.

biopython

Official git repository for Biopython (converted from CVS)

blend4j

blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

blend4j

blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

brew-docker

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bwa-mem

Galaxy wrapper for bwa mem

chaussette

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clj-blend

Clojure library for interacting with Galaxy, CloudMan, and BioCloudCentral, built on blend4j

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

cloudbiolinux-deployer

This project is meant to be used to launch a VM, configured it via a CloudBioLinux flavor (with initial focus on Galaxy and CloudMan), and upload data to it. This project is the successor of the galaxy-vm-launcher.

cloudman

git repo tracking the Galaxy project's CloudMan mercurial repository at https://bitbucket.org/galaxy/cloudman

cloudman_openstack_bootstrap

This project contains a set of scripts and config files I am using to configure CloudMan for MSI's private OpenStack cloud.

collectl

Fork of collectl taliored for applications at MSI.

common-workflow-language

Repository for CWL Specfications

conda-iuc

Conda recipes maintained by the Galaxy IUC.

cv

The source code for my CV/resume.

cwl2script

Compile CWL workflow to shell script

cwltool

Common Workflow Language reference implementation

devteam2git

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devteamdevshedtest1

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devteamtest2

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devteamtest3

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distributed-collectl-parser

A distributed CollectL parsing system for use with msi-software-accounting project.

docker-galaxy-stable

Docker Images tracking the stable Galaxy releases.

docker-ipython-notebook

IPython running in a docker container. This image can be used to integrate IPython into Galaxy

docker-jupyter-notebook

:whale: :microscope: :books: Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy

docker-recipes

Dockerfiles to build Galaxy images

docker-toolshed

Base image for ToolShed installs.

emma4j5

A fork of the popular Java code coverage tool EMMA that adds additional functionality to support Java 5+ language features.

ephemeris

Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.

europe2013

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exon-exon-junction

Updates to the Putative Exon-Exon junction database creation code found here: http://www.zcni.zju.edu.cn/en/download.htm

fabric

Simple, Pythonic remote execution and deployment.

fleeqtk

Those sequences are on fleeq - the toolkit

galaxy

Galaxy Github repository BETA 2. May be destroyed and recreated if additional post-conversion problems are found (but post-conversion commits on this repo will be reapplied to any recreations). Full details:

galaxy-2

A new, betterer Galaxy.

galaxy_blast

Galaxy wrappers for NCBI BLAST+ and related BLAST tools.

galaxy-bootstrap

A simple Java package for downloading and configuring Galaxy. Initial work is a framework to test blend4j.

galaxy-central

Deprecated repository GOTO https://github.com/galaxyproject/galaxy

galaxy-community-qa

The project is meant to provide some formal support for diverse community QA efforts - including defining interfaces and responsibilities as well as providing computational infrastructure for testing.

galaxy-dist

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galaxy-downloads

Misc. Galaxy related downloads.

galaxy-examples

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galaxy-hub

Galaxy project website, aka Galaxy Community Hub

galaxy-ipython

IPython Integration into Galaxy

galaxy-ipython-machine

Packer recipe for building demo Galaxy IPython boxes.

galaxy-lib

Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library.

Galaxy-M

Metabolomics Tools for Galaxy

galaxy-rstudio

RStudio integration into Galaxy

galaxy-rstudio-machine

Packer recipe for building demo Galaxy RStudio boxes.

galaxy-selenium

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galaxytools

Galaxy Tool wrappers

galaxy_tools

My Galaxy Wrappers

galaxy-vagrant

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Galaxy-XSD

Galaxy XML tool wrapper XSD

gcc2014_demo

Tools and Dockerfile for GCC 2014 "Demo"

globus-cookbook

Cookbook for installing globus

gravity-webapp

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gxformat2

Galaxy Workflow Format 2

gxtesttools

Test Galaxy Tools for Testing Travis Testing.... Testing.

h5py

HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

homebrew-platform

Tap for installing platform-brew extensions to brew.

homebrew-science

Scientific formulae for the Homebrew package manager

homebrew-science-test1

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homebrew-science-versions

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homebrew-tests

Moved to https://github.com/jmchilton/platform-brew

homebrew-toolshed

The Galaxy Tool Shed (toolshed.g2.bx.psu.edu) converted to a Homebrew tap.

horizon

Horizon is the dashboard for OpenStack; based on a Django module called django-openstack. Both the django-openstack module as well as a reference implementation of a fully functional Django site called openstack-dashboard are part of this project.

infrastructure-playbook

Ansible playbook for managing Galaxy infrastructure. For the playbook managing Galaxy itself, see https://github.com/galaxyproject/usegalaxy-playbook/

ipython_notebooks

My IPython notebooks ... just for demos since I don't know how to do science stuff.

jgalaxy

A Java/Swing front-end to Galaxy (http://galaxyproject.org).

jmchilton.net

Code powering jmchilton.net

jobs-dsl-test

A test of Jenkins Job's DSL

jqgrid-rails3

This plugin allows you to add jQuery datagrids very easily to your Rails applications.

just-dockerfiles

This project is an integrated test framework - tying together Jenkins testing and reporting with simple, unstructured jobs driven by Docker (Dockerfiles, Docker images, or docker-compose set ups), structured YAML metadata about tests.

libcloud

Mirror of Apache libcloud (incubating)

linuxbrew

A fork of Homebrew for Linux

linuxbrew-docker-trials

Random notes on my failing to get linuxbrew standalone up and running locally.

lorikeet

A Javascript MS/MS spectrum viewer (fork of http://code.google.com/p/lorikeet)

lwr

Github mirror of https://bitbucket.org/jmchilton/lwr.

mina-sshd

Mirror of Apache MINA SSHD

minecraft-mod-tutorial

Walking Minecraft tutorials with my son.

msi_appdev_puppet

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msi_hello_cloud_python

A simple python project demonstrating how to interact with MSI's cloud resources via the python library libcloud.

msi_software_accounting

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msi_software_accounting_scripts

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mzServer

My fork of mzServer (http://sourceforge.net/p/mzserver/home/mzServer/) updated to target the latest multiplierz changes and allow running under Wine on Linux.

openstack-cookbooks

Cookbooks for Openstack

p4

Proper Prior PR Planning

pepnovo

My local changes to PepNovo (http://proteomics.ucsd.edu/Software/PepNovo.html)

peptide-shaker

My fork of peptide-shaker (http://code.google.com/p/peptide-shaker)

picard

Galaxy wrappers for Picard tools

pico_galaxy

Galaxy tools and wrappers for sequence analysis

planemo

Command-line utilities to assist in developing tools for the Galaxy project.

planemo-extended-tests

Repo for CI of extended Planemo testing.

planemo-machine

A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.

planemo-machine-web

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planemo-workflow-test-template

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prodbiocloud

Guide to building and deploying production Galaxy instances with CloudMan and CloudBioLinux

protbiocloud

Documentation on using CloudBioLinux for Mass Spectrometry and Proteomic Analysis

proteomics-wine-env

The project lets you package up a Wine environment into a single shell script for distribution to other Linux instances or users.

proteowizard-wine-packager

Builds linux packages for proteowizard installed via wine

protvis

A fork proteomics-visualise https://bitbucket.org/Andrew_Brock/proteomics-visualise

psm-eval

Python application and framework for reanalyzing peptide-spectrum-matches (PSMs).

pulsar

Pulsar is the distributed job execution application built for Galaxy (http://galaxyproject.org/).

puppet-biocloudcentral

Puppet configuration for biocloudcentral.

puppet-jmchilton

John Chilton's puppet repository powering jmchilton.net and related sites and servers.

puppetlabs-apache

Puppet Labs Apache module

puppetlabs-glance

module for managing glance

puppetlabs-keystone

Modules for managing installation/configuration of OpenStack's identity management

puppetlabs-mysql

getting ready to publish our mysql module!

puppetlabs-nova

Integration work for Puppet and Nova.

puppetlabs-rabbitmq

RabbitMQ Puppet Module

puppet-lwr

A puppet module managing LWR (https://bitbucket.org/jmchilton/lwr/) servers.

puppet-module-template

Template puppet module to build new modules from.

puppet-postgresql

A Puppet module for managing postgres

puppet-python

Puppet module for installing and managing python, pip, virtualenvs and Gunicorn virtual hosts.

puppet-rvm

A puppet module for installing and using RVM (Ruby Version Manager)

puppet-tint

Puppet modules for the TINT project (https://github.com/jmchilton/TINT).

puppet-tomcat

Puppet module for Apache Tomcat

puppet-vcsrepo

Support for source control repositories

pymz5

A python library to access mz5 mass spectrometry data files

pymz5-failed-attempt

Failed attempt at creating project that builds on h5py code.

pyre-to-regexp

Converts Python-like (re) regular expressions to JavaScript RegExp instances

pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

python-mesos-examples

Standalone Python examples for Apache Mesos.

pyyayaml

A Python library for parsing YAYAML.

scaffold-packager

This project contains a script to package a Proteome Software's Scaffold into an OS package.

schema_salad

Semantic Annotations for Linked Avro Data

scibrew-core-versions

Experiments in a core set of potentially versioned dependencies on top of Homebrew core for use by scientific applications.

sequence_utils

Galaxy's sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.

sequest-pvm-packager

This project contains a script to package a Linux cluster version of sequest27 into an OS package.

shed

alternative toolshed for galaxy

shed2tap

Python script to transcribe Galaxy ToolShed packages into a tap for resuse with Homebrew.

shed-brew

Homebrew/linuxbrew extensions that provide CLI syntactic sugar for installing Tool Shed sync-ed tap recipes.

shedclient-beta

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SnpEffect

My local mirror of SVN repository for SnpEffect (http://svn.code.sf.net/p/snpeff/code/SnpEffect/trunk/).

standards

Documentation for standards and best practices from the Galaxy IUC

starforge

Build Galaxy dependencies, wheels, and other things, in Docker (and other things)

SuperHirn

Fork of SuperHirn with local changes to get it compiling under Ubuntu 12.04

swift

Swift user interface to run multiple proteomics search engines + scaffold

tempest

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TINT

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toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

tools-cummerbund

JJ's Galaxy cummeRbund work

tools-devteam

Repository encapsulating a set of Galaxy tools mostly written by the Galaxy Team.

tools-iuc

Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission

training-material

A collection of training material from offered Galaxy courses

vm-launcher

This project is meant to encompass a simple python API on top of libcloud, fabric, and vagrant to manage building and deploying cloud images.

vm-launcher-skeleton

An outline for a python project to get started with vm-launcher quickly.

vm-launcher-transfer-test

An small vm-launcher project to test file transfer component in isolation.

writing

Posters, etc...

yacaqueryservice

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Commits To