dpmccabe

[
    {
        "name": "age",
        "type": "integer",
        "description": "age of donor at time of sampling",
        "required": false,
        "unique": false
    },
    {
        "name": "age_category",

dpmccabe

# based on https://github.com/Ensembl/ensembl-vep/blob/release/112/docker/Dockerfile
# but with everything installed as root (to make it easier to run on files in /cromwell_root)
ARG BRANCH=release/113

###################################################
# Stage 1 - docker container to build ensembl-vep #
###################################################
FROM ubuntu:22.04 AS builder

# Update aptitude and install some required packages

dpmccabe

version 1.0

task PreprocessIntervals {
    input {
      File? intervals
      File? blacklist_intervals
      File ref_fasta
      File ref_fasta_fai
      File ref_fasta_dict
      Int? padding

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;

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

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

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

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

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

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

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