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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') { | |
environment { | |
// 'This value is exported to all commands in this stage' | |
AWESOME_BUILD = "${env.BUILD_ID + '/working'}" | |
} | |
steps { | |
sh 'mkdir -p $AWESOME_BUILD' |
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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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#!/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 |
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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): |
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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 |
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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) |
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import os | |
import shutil | |
import tempfile | |
import textwrap | |
import unittest | |
class TestFileReader(unittest.TestCase): | |
def setUp(self): | |
self.tempdir = tempfile.mkdtemp() |
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{ | |
"$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"] |
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