zorbax

#!/usr/bin/perl -w

$version              = localtime((stat($0))[9]);
$circos_compatibility = '0.69-3';

$| = 1;

use POSIX;
use Getopt::Long;
use Bio::SearchIO;

zorbax

for i in $(ls *rst)
do
  filename="${i%.*}"
  echo "Converting $i to $filename.md"
  pandoc $i -f rst -t markdown -o $filename.md`
done

zorbax

cd $HOME/bin
perl -MNet::FTP -e \
    '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
    $ftp->login; $ftp->binary;
    $ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf - && rm edirect.tar.gz
export PATH=$PATH:$HOME/bin/edirect >& /dev/null && ./edirect/setup.sh

echo "export PATH=\$PATH:\$HOME/bin/edirect" >> $HOME/.bash_profile

zorbax

zorbax

#!/usr/bin/env python
import os
import sys
import argparse
import json
import math
import subprocess
from urllib2 import Request, urlopen, URLError

zorbax

1. Clone your fork:

git clone https://github.com/zorbax/REPO.git

2. Add remote from original repository in your forked repository:

cd REPO
git remote add upstream https://github.com/ORIGINAL-DEV-USERNAME/REPO.git

git fetch upstream

zorbax

sudo apt-get update && sudo apt-get install -y build-essential unzip cmake \
     gcc g++ automake make zlib1g-dev libncurses5-dev libboost-all-dev zlibc libxml2

mkdir -p $HOME/bin && cd $_
wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-tar.zip
unzip bcl2fastq2-v2-20-0-tar.zip
tar -zxvf bcl2fastq2-v2.20.0.422-Source.tar.gz
rm bcl2fastq2-v2-20-0-tar.zip bcl2fastq2-v2.20.0.422-Source.tar.gz

cat <<EOF >> $HOME/.bashrc

zorbax

#!/bin/bash

if [ -z "$1" ]; then
        echo
        echo usage: $0 network-interface
        echo
        echo e.g. $0 eth0
        echo
        exit
fi

zorbax

library(BaseSpaceR)

args<-commandArgs(TRUE)

TOKEN<- args[1]
ID<- args[2]

aAuth<- AppAuth(access_token = TOKEN)
selProj <- Projects(aAuth, id = ID, simplify = TRUE) 

zorbax

#!/bin/bash

input=$1
format=$( file $input | cut -d ' ' -f2 )

if [[ $format == "gzip" ]]; then
  zless $input | head -100 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | \
    awk 'BEGIN{min=100;max=0;} {for(i=1;i<=NF;i++) {if($i>max) max=$i;
    if($i<min) min=$i;}}END{if (max<=74 && min<59) print "Phred+33";
    else if(max>73 && min>=64) print "Phred+64";