I hereby claim:
- I am mlin on github.
- I am mlin (https://keybase.io/mlin) on keybase.
- I have a public key ASCO-NadYMiwqGxb9_4cD-VFjMbVqrk7ors-n9seZl_A5wo
To claim this, I am signing this object:
/* | |
$ uname -a | |
Linux coderuler 3.2.0-24-generic #39-Ubuntu SMP Mon May 21 16:52:17 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux | |
$ node -v | |
v0.6.18 | |
$ echo "console.log('foobar'); process.exit(0);" > foo.js | |
$ node node_cluster_child_process.js | |
child stderr > |
(* | |
ocamlfind ocamlopt -o netclient_https_threads -thread -linkpkg -package threads,netclient,ssl,equeue-ssl netclient_https_threads.ml | |
http://docs.camlcity.org/docs/godipkg/3.12/godi-ocamlnet/doc/godi-ocamlnet/html/Https_client.html | |
*) | |
open Printf | |
module HTTP = Http_client | |
module HTTPS = Https_client | |
;; |
* 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 |
["Human","hg19"], | |
["Chimp","panTro4"], | |
["Gorilla","gorGor3"], | |
["Orangutan","ponAbe2"], | |
["Gibbon","nomLeu3"], | |
["Rhesus","rheMac3"], | |
["Crab_eating_macaque","macFas5"], | |
["Baboon","papHam1"], | |
["Green_monkey","chlSab1"], | |
["Marmoset","calJac3"], |
#!/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 |
I hereby claim:
To claim this, I am signing this object:
#!/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. |
# 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 |
#!/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() |
version 1.0 | |
task split_vcf_for_spark { | |
# Quickly split a large .vcf.gz file into a specified number of compressed partitions. | |
# | |
# Motivation: calling SparkContext.textFile on a single large vcf.gz can be painfully slow, | |
# because it's decompressed and parsed in ~1 thread. Use this to first split it up (with a | |
# faster multithreaded pipeline); then tell Spark to parallel load the data using textFile on a | |
# glob pattern. | |
# |