laserson

#! /usr/bin/env fish

set target_pids (pgrep caffeinate)
set num_pids (count $target_pids)

if test $num_pids -eq 0
    caffeinate -d -t 43200
else
    for target_pid in $target_pids
        kill $target_pid

laserson

from opentrons import robot, containers, instruments

robot.connect(robot.get_serial_ports_list()[0])
robot.home()

tiprack200 = containers.load('tiprack-200ul', 'C2')
trash = containers.load('point', 'D2')
p200 = instruments.Pipette(axis='a',               
                           max_volume=200,
                           min_volume=20,

laserson

import json
from copy import deepcopy
from itertools import product
from collections import OrderedDict

all_wells = ['{}{}'.format(r, c) for c in range(1, 13) for r in 'ABCDEFGH']

with open('_containers_create.json.bak','r') as ip:
    obj = json.load(ip)

laserson

import pandas as pd
from airtable import airtable


metadata = pd.read_table(metadata_path, sep=',', header=0, index_col=None)
at = airtable.Airtable(base_id, api_key)
ibd_records = at.get('sample', filter_by_formula='AND(project = "cho-ibd", phenotype = "")')['records']

for record in ibd_records:
    if (metadata.local_sample == record['fields']['sample_id']).sum() != 1:

laserson

Drag and drop desired messages to directories (e.g., archived/).

Convert directory to mbox file

./eml2mbox.py archived archived.mbox

Follow directions here to upload via Gmail API

https://github.com/google/import-mailbox-to-gmail

laserson

package com.cloudera.science.throwaway;

public class ThrowAway {
    private String datum = "Howdy!";

    public ThrowAway() { }

    public String response() {
        return "Goodbye!";
    }

laserson

import org.bdgenomics.formats.avro.AlignmentRecord
import org.bdgenomics.adam.rdd.ADAMContext._

val bamFile = "/Users/laserson/repos/adam/adam-core/src/test/resources/artificial.sam"
val reads = sc.adamLoad[AlignmentRecord, Nothing](bamFile)

reads.first()
/*
java.lang.IncompatibleClassChangeError: Implementing class
	at java.lang.ClassLoader.defineClass1(Native Method)

laserson

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-33-9be617700fcd> in <module>()
      6     t = ax.plot(times, events, lw=1, c=random_color())
      7 ax.set_yscale('log')
----> 8 IPython.core.pylabtools.print_figure(fig)

/usr/lib/python2.6/site-packages/IPython/core/pylabtools.pyc in print_figure(fig, fmt)
    108         fmt = 'png'
    109     fig.canvas.print_figure(bytes_io, format=fmt, bbox_inches='tight',

laserson

laserson

Building Spark for PySpark use on top of YARN

Build Spark on local machine (only if using PySpark; otherwise, remote machine works) (http://spark.apache.org/docs/latest/building-with-maven.html)

export MAVEN_OPTS="-Xmx2g -XX:MaxPermSize=512M -XX:ReservedCodeCacheSize=512m"
mvn -Pyarn -Phadoop-2.4 -Dhadoop.version=2.4.0 -DskipTests clean package

Copy the assembly/target/scala-2.10/...jar to the corresponding directory on the cluster node and also into a location in HDFS.