23jodys

vagrant init <base box>
vagrant up
vagrant ssh
# Do your customizations here
# yum -y install blah blah
# don't forget to clean up, yum clean all
# Reset the insecure key
dd if=/dev/zero of=/EMPTY bs=1M; rm -f /EMPTY
curl https://raw.githubusercontent.com/mitchellh/vagrant/master/keys/vagrant.pub > ~/.ssh/authorized_keys
exit

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pipeline {
  agent any
  stages {
    stage('Example') {
      steps {
        // interpolated by the shell
        sh 'echo Shell $PWD' 
        // interpolated by the shell
        sh '''echo Shell $PWD'''
        // interpolated in this file by Groovy

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pipeline {
  agent any
  stages {
    stage('Example') {
      environment {
        // 'This value is exported to all commands in this stage'
        AWESOME_BUILD = "${env.BUILD_ID + '/working'}"
      }
      steps {
        sh 'mkdir -p $AWESOME_BUILD'

23jodys

#!/usr/bin/env python
""" Holds logic for TestReporter objects """

__author__ = "Mike 'Monty' Montgomery"
__copyright__ = "Copyright 2015, ArcherDX"
__credits__ = ["Mike 'Monty' Montgomery, Jody 'JodyStephens' Stephens"]
__license__ = "To Scribe"
__version__ = "0.1"
__maintainer__ = "Mike 'Monty' Montgomery"
__email__ = "mmontgomery@archerd.com"

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# tests

23jodys

from verum.common import ITestRecord, IValidationRecord, getPass
logger = logging.getLogger(__name__)

class VariantTestRecord(ITestRecord):
    def __init__(self, variant, success=False):
        self.variant = variant
        self.success = success
        self.ident = "{}:{}".format(variant.CHROM, variant.POS)

class VariantMatch(VariantTestRecord):

23jodys

FC_1_CONSENSUS	TCGGCGCCTTTCGAGCAGTACTCCCCGGGTGGCCAGGACACCCCCAGCTCCAGCTCCTCAGGGGACGACTCCGTGTTTGCCCACGACCTGCTGCCCCCGGCCCCACCCATTTAAGGAGTCGGCCTTGAGGAAGCAGTCCTTATACCTCAAGTT
FC_1_CONSENSUS	CGCCTTTCGAGCAGTACTCCCCGGGTGGCCAGGACACCCCCAGCTCCAGCTCCTCAGGGGACGACTCCGTGTTTGCCCACGACCTGCTGCCCCCGGCCCCACCCATTTAAGGAGTCGGCCTTGAGGAAGCAGTCCTTATACCTCA
chr4_1808384-1808403_11_R1_full_results.txt
FC_1_CONSENSUS	CCTGTACATGATCATGCGGGAGTGCTGGCATGCCGCGCCCTCCCAGAGGCCCACCTTCAAGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGACGTAAAGGCGACACAGGAGGAGAACCGGGAGCTGAGGAGCAGGTGTGAGGAGCTCCACGGGAAGAACCTGGAACTGGGGAAGATCATGGACAGGTTCGAAGAGGTTGTGT
FC_1_CONSENSUS	TACATGATCATGCGGGAGTGCTGGCATGCCGCGCCCTCCCAGAGGCCCACCTTCAAGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGACGTAAAGGCGACACAGGAGGAGAACCGGGAGCTGAGGAGCAGGTGTGAGGAGCTCCACGGGAAGAACCTGGAACTGGGGAAGATCATGGACAGGTTCGAAGAGGTT
chr4_1808384-1808403_12_R1_full_results.txt
FC_1_CONSENSUS	CCTGTACATGATCATGCGGGAGTGCTGGCATGCCGCGCCCTCCCAGAGGCCCACCTTCAAGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGACGTGCCAGGCCCACCCCCAGGTG

23jodys

class SampleHighlight(object):
  def __init__(self, job_id, sample_name, field1):
    errors = []
    if not job_id.startswith("JOB_ID"):
      errors.append("STRUCTURAL FAILURE: bad job_id")
      
    try:
      self._check_sample_name(sample_name)
    except Exception as error:
      errors.append(error.message)

23jodys

import os
import shutil
import tempfile
import textwrap
import unittest

class TestFileReader(unittest.TestCase):

    def setUp(self):
        self.tempdir = tempfile.mkdtemp()

23jodys

{
	"$schema": "http://json-schema.org/schema#"
	"definitions":{
		"target": {
			"type": "object",
			"properties": {
				"primer_size_min": {"type": "number", "minimum": 10, "maximum": 30},
				"primer_size_max": {"type": "number", "minimum": 20, "maximum": 40}
			},
			"required": ["primer_size_min", "primer_size_max"]