maasha

# Function to assert no difference between
# two given files.
function assert_no_diff
{
    local src=$1
    local dst=$2

    if [ ! -f $src ]; then
        echo_red "FAIL"
        log "FAIL"

maasha

#!/usr/bin/env ruby

require 'biopieces'

p = BP.new.
read_fastq(input: "in1.fq", input2: "in2.fq").
clip_primer(primer: "GTGCCAGCMGCCGCGGTAA",  direction: :forward, mismatch_percent: 20, search_distance: 50).
clip_primer(primer: "GGACTACHVGGGTWTCTAAT", direction: :forward, mismatch_percent: 20, search_distance: 100).
trim_primer(primer: "GTGCCAGCMGCCGCGGTAA",  direction: :forward, mismatch_percent: 20, overlap_min: 1).
trim_primer(primer: "GGACTACHVGGGTWTCTAAT", direction: :forward, mismatch_percent: 20, overlap_min: 1).

maasha

#!/usr/bin/env ruby

require 'set'
require 'google_hash'
require 'benchmark'

set    = Set.new
hash   = Hash.new(0)
ghashd = GoogleHashDenseIntToInt.new
ghashs = GoogleHashSparseIntToInt.new

maasha

require 'spec_helper'

describe "AuthenticationPages" do
  subject { page }

    describe "authorization" do
      describe "for non-signed-in users" do
        let(:user) { FactoryGirl.create(:user) }

        describe "when attempting to visit a protected page" do

maasha

#!/usr/bin/env ruby

class Cmd
  def cat(file)
  end 
  
  def grep(pattern)
  end 
end

maasha

QIIME-1.6.0 install
===================
  Documentation: http://qiime.org/install/install.html

  home    = /home/maasha/
  install = /home/maasha/install
  prefix  = /home/maasha/install/QIIME1.6/
  source  = /home/maasha/install/QIIME1.6/src/

  bashrc  = /home/maasha/install/QIIME1.6/bashrc

maasha

maasha@orsted:~$ print_qiime_config.py -t

System information
==================
         Platform:      linux2
   Python version:      2.7.3 (default, Jan 28 2013, 09:50:08)  [GCC 4.4.5]
Python executable:      /disk/orsted/install/maasha/QIIME1.6/bin/python

Dependency versions
===================

maasha

maasha@mel:~$ mtr -r newton
HOST: mel.local                   Loss%   Snt   Last   Avg  Best  Wrst StDev
  1.|-- 10.52.32.1                 0.0%    10    0.6   0.6   0.5   0.7   0.0
  2.|-- 192.38.100.193             0.0%    10    2.6   2.3   1.1   4.8   1.1
  3.|-- life3-26.net.ku.dk         0.0%    10    2.3   2.5   1.1   6.3   1.5
  4.|-- adm3-28.net.ku.dk          0.0%    10    1.2   2.3   1.2   3.9   0.9
  5.|-- kua3-15.net.ku.dk          0.0%    10    1.5   2.0   1.1   2.8   0.6
  6.|-- 172.20.120.17              0.0%    10    1.7   1.8   1.3   4.3   0.9
  7.|-- ???                       100.0    10    0.0   0.0   0.0   0.0   0.0
  8.|-- ???                       100.0    10    0.0   0.0   0.0   0.0   0.0

maasha

maasha@mel:~$ ssh -vv newton date 2>&1 | perl -MTime::HiRes -ne 'use Time::HiRes; $s=Time::HiRes::time(); print "$s.$ms $_"'
1359540642.5785. OpenSSH_5.6p1, OpenSSL 0.9.8r 8 Feb 2011
1359540642.57853. debug1: Reading configuration data /Users/maasha/.ssh/config
1359540642.57854. debug1: Applying options for newton
1359540642.57854. debug1: Reading configuration data /etc/ssh_config
1359540642.57855. debug1: Applying options for *
1359540642.57855. debug2: ssh_connect: needpriv 0
1359540642.57856. debug1: Connecting to newton.binf.ku.dk [130.225.211.96] port 24222.
1359540642.57856. debug1: Connection established.
1359540642.57856. debug2: key_type_from_name: unknown key type '-----BEGIN'

maasha

#!/bin/bash

function run()
{
    cmd=$1

    if error=$($cmd); then
        echo "OK"
    else
        echo "FAIL"