Mike Lin mlin

I hereby claim:

To claim this, I am signing this object:

	#!/usr/bin/env python3

	import sys
	import time
	import docker
	import multiprocessing
	from argparse import ArgumentParser, REMAINDER

	def swarmsub(image, command=None, cpu=1, mounts=None):
	client = docker.from_env()

	#!/usr/bin/env python
	#
	# Initializes a git repository with some suggested best practices for DNAnexus
	# WDL workflow development & continuous integration. Run
	# dxWDL_ci_init.py hello_world
	# to create a subdirectory with that name, initialized as a local git repo,
	# with the following which you can then customize:
	#
	# hello_world.wdl
	# Trivial WDL workflow template.

	#!/usr/bin/env python
	#
	# dx-yml-build: transcodes dxapp.yml to dxapp.json and then runs `dx build`
	# with command-line arguments passed through.
	#
	# Requires PyYAML (apt-get install python-yaml OR pip install pyyaml)

	import os, sys
	import yaml, json

	* index (vg_index:main) (failed) job-Bk01J1Q0QpJ6F3BZv5ZyjBBq
	mlin 2015-11-08 19:44:06 (runtime 12:57:05)
	2015-11-09 11:33:40 index ALERT This job has been restarted due to UnresponsiveWorker from running this job
	2015-11-09 11:33:49 index INFO Logging initialized (priority)
	2015-11-09 11:33:50 index INFO Downloading bundled file gcc4.9_runtime_debs.tar
	2015-11-09 11:33:51 index STDOUT >>> Unpacking gcc4.9_runtime_debs.tar to /
	2015-11-09 11:33:51 index INFO Downloading bundled file vg_bundle.tar.gz
	2015-11-09 11:33:52 index STDOUT >>> Unpacking vg_bundle.tar.gz to /
	2015-11-09 11:33:53 index INFO Installing apt packages libjansson4, dx-toolkit
	2015-11-09 11:33:57 index INFO Setting SSH public key

	#!/usr/bin/env python
	#
	# Initializes a git repository with some suggested best practices for DNAnexus
	# workflow development & continuous integration. Run dx-ci-init.py in the root
	# of your git repository; it creates the following, which you should then
	# customize as you like:
	#
	# applets/hello-world
	# Trivial applet template which you can build on or copy.
	#

	require(ggplot2)
	require(data.table)
	require(compiler)

	# First run LASTZ to produce MAF output. Options for matching near-identical assemblies: --notransition --seed=match15 --step=10 --hspthresh=100000 --gapped --ydrop=3400 --gappedthresh=400000 --ambiguous=iupac --allocate:traceback=200M
	# Then we postprocess the MAF with: cat alignments.maf \| awk 'NF' \| tr -s " " \| cut -d ' ' -f1-6 \| paste - - - \| tr " " "\t" \| tr "=" "\t" \| cut -f 3,5-9,11-15 \| gzip -c > alignments.gz
	# read and filter hits
	fn <- "alignments.gz"
	all.hits <- read.delim(gzfile(fn),header=FALSE)
	colnames(all.hits) <- c("score","target","tpos","thitlen","tstrand","tlen","query","qpos","qhitlen","qstrand","qlen")

	# Dockerfile for PhyloCSF using OpenBLAS to take advantage of vector
	# instructions (AVX). On supported processors, this can significantly speed up
	# PhyloCSF (25-50%) compared to the default GSL BLAS.
	# Example usage:
	# docker build -t mlin:PhyloCSF https://gist.githubusercontent.com/mlin/5ea4ca5d2a2a198e5659/raw/Dockerfile
	# docker run -v /path/to/host/data:/data mlin:PhyloCSF 29mammals /data/input.fa
	# PhyloCSF homepage: https://github.com/mlin/PhyloCSF/wiki
	FROM ubuntu:trusty
	MAINTAINER Mike Lin <mlin@mlin.net>
	RUN apt-get update

	# Basic Dockerfile for PhyloCSF.
	# Example usage:
	# docker build -t mlin:PhyloCSF https://gist.githubusercontent.com/mlin/31c0a7623f99d3bf3222/raw/Dockerfile
	# docker run -v /path/to/host/data:/data mlin:PhyloCSF 29mammals /data/input.fa
	# PhyloCSF homepage: https://github.com/mlin/PhyloCSF/wiki
	FROM ubuntu:trusty
	MAINTAINER Mike Lin <mlin@mlin.net>
	RUN apt-get update
	RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-suggests --no-install-recommends ca-certificates software-properties-common time git build-essential gfortran
	RUN add-apt-repository ppa:avsm/ppa