wckdouglas

wckdouglas

Computing environment setup guide for chromebooks

Douglas Wu

---

This is a note for myself to setup a developer environment on chromebook without using crouton (Running Linux GUI on chromeOS). I chose chromebrew since it is just a CLI interface and doesn't require running anything on top of any apps. And I am also a fan of miniconda, which works well on the linux kernal of ChromeOS.

1. Get into developer mode, go to terminal and enter shell.

2. Install chromebrew:

wckdouglas

def read_fastq(file_fq):
    """
    takes a fastq file as input
    yields idSeq, sequence and score
    for each fastq entry
    learned from:
    http://codereview.stackexchange.com/questions/32897/efficient-parsing-of-fastq
    """

    line_count = 0

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packages <- c('readr', 'dplyr', 'devtools', 'rcpp', 'stringr', 'tidyr','ggplot2','bit64')
install.packages(packages)

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#!/usr/bin/env python

from bs4 import BeautifulSoup
import pandas as pd
from HTMLParser import HTMLParseError
import os

def extractTable(soup):
    data = []
    JOB_num = [word for word in soup.getText().split(' ') if word.startswith('JA')][1]

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#!/usr/bin/env python

from twilio.rest import TwilioRestClient
import paramiko
import os
import sys
import time

def sendMessage(job):
    #twilio

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#!/bin/bash

if [[ $# -ne 1 ]]
then
    echo Need commit message!!
    exit
else
    git commit -am "$1"
fi

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{
	"filters":[
		{ "id":"firstPairForward",
			"alignmentFlag" : "99" },
		{"id":"firstPairReverse",
			"alignmentFlag" : "83"},
		{"id":"secondPairForward",
			"alignmentFlag" : "163"},
		{"id":"secondPairReverse",
			"alignmentFlag" : "147"}

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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
backports=1.0=py27_0
backports_abc=0.4=py27_0
bamtools=2.4.0=3
bcftools=1.3=0
bedops=2.4.19=0
bedtools=2.25.0=1
bioconductor-annotationdbi=1.32.3=0

wckdouglas

#!/bin/bash

#install pathogen
mkdir -p ~/.vim/autoload ~/.vim/bundle && \
	curl -LSso ~/.vim/autoload/pathogen.vim https://tpo.pe/pathogen.vim

echo '
execute pathogen#infect()
syntax on
filetype plugin indent on