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print("Still Alive!")

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#! /usr/bin/python
import argparse
import csv
import requests
import re
from bs4 import BeautifulSoup
import pickle


supported_protocols = [

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#! /usr/bin/python
import argparse
from random import randrange, randint, shuffle 
from prettytable import PrettyTable
import os


EMPTY_VALUE = " "

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#!/bin/bash

#
# A convenience shell script to call criu for checkpointing and restoring
# a Docker container.
#
# This script saves the user from having to remember all the command
# line options, some of which are very long.  Note that once Docker
# has native support for checkpoint and restore, there will no longer
# be a need for this particular shell script.

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#define _GNU_SOURCE
#include <sched.h>
#include <stdio.h>
#include <stdlib.h>
#include <sys/wait.h>
#include <unistd.h>
#define STACK_SIZE (1024 * 1024)

static char child_stack[STACK_SIZE];

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VARCALLER Statistics Package

• This directory contains tools and scripts for automated, local analysis and evaluation of varcaller change to a pipeline.
• As time progresses, these tools should allow R&D departments add, remove, perform parameter searches and develop quality functions without needing their scientific department.

Usage

• run GIAB son sample through the varcaller
• get the bam.bed file from the mapper
• get the current output vcf of the pipeline

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#! /usr/bin/python3
from github import Github, GithubException
from prettytable import PrettyTable
import sys

def printProgressBar (iteration, total, prefix = 'Progress:', suffix = 'Complete', total_length = 78, fill = '█'):
    percent = 100 * (iteration / float(total))
    percent_str = ("{0:.1f}").format(percent)
    length = total_length - len(prefix) - len(suffix) - len (percent_str)
    filledLength = int(length * iteration // total)

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#! /bin/sh

export SENTIEON_PROJECT_HOME=/home/ubuntu/sentieon 
export SENTIEON_LICENSE=$SENTIEON_PROJECT_HOME/emedgene_eval.lic
export SENTIEON_BIN=$SENTIEON_PROJECT_HOME/sentieon-genomics-201808.03/bin/sentieon

export REFERENCE=/opt/data/ref/Human/Hg19/genome_ref/hg19.fa #$SENTION_DATA_DIR/reference/hg19/hg19.fa

export BED_FILE=/opt/data/input/UNIQUE_Agilent_130_5.bed

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Sentieon script for basic DNAseq (FastQ to VCF) as instructed on https://support.sentieon.com/manual/DNAseq_usage/dnaseq/

How To Use This Script

• Put it wherever, it's all based on absolute paths
• Open it in an editor of your choosing
• Fill in all the in the exports section
• Change (or leave as is) the bwt_max_mem and NUMBER_THREADS env vars to suite your needs
• Make sure to raise file descriptor limits to the allowed max by running ulimit -n unlimited
• Run it

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language: c
compiler: gcc
sudo: required
install: make clean && make
before_script:
  - git clone https://github.com/antirez/redis.git
  - cd redis
  - make
  - sudo pip install redis
  - cd ..