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Jay R Bolton jayrbolton

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jayrbolton / workflowz.py

Last active January 14, 2019 22:55

	# Define a docker workflow (independent of KBase)
	# - output and input files
	# - minimum node requirements for a job
	# - whether to exit on any failure or continue on failure
	# - pass through environment variables
	# - htcondor, etc backend
	# - automatically figure out serial and concurrent execution based on task input and output


	def subsample():

jayrbolton / pypiper.py

Created February 6, 2019 23:09

	# A task is a docker image, a command, and optional hardware prefs
	# A pipeline is a collection of sequential or parallel tasks with a shared volume mount
	# Pipelines are submitted to HTCondor

	# A small application layer would handle the job submission to HTCondor,
	# pulling docker images and running containers with correct mounts and settings

	# Define an HTCondor job with a docker image, command, and node requirements or preferences
	subsample = Task(
	image='jgi/subsample',

jayrbolton / list-of-counters-challenge.md

Last active March 21, 2019 18:01

List-of-counters UI challenge for evaluating frameworks

Create a counter component with

jayrbolton / jgi_readqc.wdl

Created March 25, 2019 17:20

jgi qc pipeline for shifter

	workflow jgi_read_qc
	{
	File raw_fastq
	Array[String] sketch_dbs = [ "nt", "refseq", "silva" ]

	call subsample
	{
	input:
	infile=raw_fastq
	}

jayrbolton / zmq_example.py

Created June 12, 2019 22:54

	import time
	import zmq
	import atexit
	import logging
	from zmq.devices import ProcessDevice
	from zmq.log.handlers import PUBHandler
	from multiprocessing import Process

	# All child processes we create
	procs = [] # type: list

jayrbolton / push_pull_threads_queue.py

Created June 24, 2019 17:43

Example of push pull workers with builtin thread queue vs zmq thread queue

	import time
	from threading import Thread
	from queue import Queue


	# Advantages:
	# - a little simpler, uses only builtins
	# - doesn't require another lib
	# Disadvantages:
	# - harder to migrate to other architectures (eg. request/reply, processes, fair share)

jayrbolton / push_pull_threads_zmq.py

Created June 24, 2019 17:43

Example of push pull workers with zmq thread queue vs builtin thread queue

	import time
	import zmq
	import zmq.devices
	from threading import Thread

	# Advantages:
	# - Easier to change the architecture around
	# - Easier to add other processes, workers, remote workers, etc
	# Disadvantages:
	# - Need a little knowledge of zmq

jayrbolton / test.s

Last active July 30, 2019 20:26

	# Register-based -- all varaibles are stored in registers. Sub-function calls are templated and expanded inline
	# Compute the nth factorial
	fun factorial n:int -> int
	\| count <- n
	$ loop while (gt count 1)
	\| count <- dec count
	\| n <- mul count n
	$ repeat
	$ return n

jayrbolton / assembly-example2.s

Last active July 30, 2019 21:29

	# Sum of multiples of `n` up to `limit
	# eg: 18 is the sum of multiples of 3 up to 10 (3, 6, 9)
	fun mul_sum n:int lim:int -> int
	\| sum <- 0
	\| counter <- 1
	\| mul <- n
	$ loop while !lt mul lim
	\| counter <- !inc counter
	\| mul <- !add mul n
	\| sum <- !add sum mul

jayrbolton / bin_tree.txt

Created August 10, 2019 05:54