dpmccabe

17:13:34.819 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/xchip/scarter/dmccabe/software/gatk-protected_e54dac3/build/libs/gatk-protected-package-e54dac3-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
[April 12, 2017 5:13:34 PM EDT] org.broadinstitute.hellbender.tools.exome.convertbed.ConvertBedToTargetFile  --input test2.bed --output test2.target  --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false
[April 12, 2017 5:13:34 PM EDT] Executing as dmccabe@ccpm.broadinstitute.org on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Version: Version:e54dac3-SNAPSHOT
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.BUFFER_SIZE : 131072
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.COMPRESSION_LEVEL : 5
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.CREATE_INDEX : false
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.CREATE_MD5 : false
17

dpmccabe

merged_fit <- alply(1:n_samp, 1, function(s) {
	h_seg_dat_new$h.capseg.d[[merge_ixs[1]]] <- unlist(h_seg_dat_new$h.capseg.d[merge_ixs])
	h_seg_dat_new$h.capseg.raw[[merge_ixs[1]]] <- unlist(h_seg_dat_new$h.capseg.raw[merge_ixs])
	h_seg_dat_new$h.capseg.annot[[merge_ixs[1]]]$pos <- unlist(lapply(h_seg_dat_new$h.capseg.annot[merge_ixs], "[[", "pos"))
	h_seg_dat_new$gh.wes.allele.d[[merge_ixs[1]]] <- do.call(cbind, h_seg_dat_new$gh.wes.allele.d[merge_ixs])
	h_seg_dat_new$gh.wes.allele.annot[[merge_ixs[1]]]$pos <- unlist(lapply(h_seg_dat_new$gh.wes.allele.annot[merge_ixs], "[[", "pos"))
	if (n_merge_hets >= 2) h_seg_dat_new$seg_phase_pr[[merge_ixs[1]]] <- 0.5
	if (n_merge_hets >= 2) h_seg_dat_new$consensus_phase[[merge_ixs[1]]] <- init_merged_consensus_phase(log_het_phase_prob_list)
	capture_em_fit_new$log.het.phase.prob[[merge_ixs[1]]] <- data_frame("x1" = rep(NA, n_merge_hets))
	capture_em_fit_new$het.phase.prob[[merge_ixs[1]]] <- capture_em_fit_new$log.het.phase.prob[[merge_ixs[1]]]

dpmccabe

library(dplyr)
library(tidyr)
library(stringr)

sort_course_codes <- function(course_codes) {
  course_with_sorting <- data_frame(course_code = course_codes) %>%
    mutate(course_code_cleaned = str_trim(tolower(str_replace_all(
      course_code, "[(\\[\\{][^(\\[\\{]+[)\\]\\}]", ""
    )))) %>%
    separate(

dpmccabe

library(RPostgreSQL)
library(pool)
library(dplyr)
library(dbplyr)

pool <- dbPool(
  drv = PostgreSQL(),
  host = Sys.getenv("DB_HOST"),
  port = 5432,
  dbname = Sys.getenv("DB_NAME"),

dpmccabe

FROM logstash:6.6.1

ADD ./logstash.conf .
ADD ./logstash.yml .
ADD ./template.json .

ENV LS_JAVA_OPTS="-Dls.cgroup.cpuacct.path.override=/ -Dls.cgroup.cpu.path.override=/ -Djava.security.egd=file:/dev/urandom $LS_JAVA_OPTS"

CMD logstash -f ./logstash.conf --path.settings=. --verbose --log.level=debug

dpmccabe

from flask import Flask

def create_app():
    app = Flask('testapp')
    
    # omitted for brevity: load app config

    # configure database
    from app.lib.db import init_engine, db_session
    init_engine(app.config['DATABASE_URI'])

dpmccabe

function doSub() {
  setTimeout(function() {
    if ($('.subButtons a.add.active').length === 0) {
      clearTimeout(doSub)
    } else {
      var el = $('.subButtons a.add.active:first')
      console.log(el.parent().parent().parent().find('a:first').text())

      $(el).click()
      doSub()

dpmccabe

heroku config -s -a from-app > ~/Desktop/env.txt
cat ~/Desktop/env.txt | tr '\n' ' ' | xargs heroku config:set -a to-app

dpmccabe

import re
from time import sleep
from typing import Any, Dict

import boto3
from zappa.cli import ZappaCLI

PROVISIONED_CONCURRENCY = 5

client = boto3.client("lambda")

dpmccabe

import { noop, safe_not_equal } from 'svelte/internal';

/** Callback to inform of a value updates. */
export type Subscriber<T> = (value: T) => void;

/** Unsubscribes from value updates. */
export type Unsubscriber = () => void;

/** Callback to update a value. */
export type Updater<T> = (value: T) => T;