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import com.twitter.bijection.avro.{GenericAvroCodec, GenericAvroCodecs}
import com.twitter.bijection.Injection
import com.twitter.chill._
import org.apache.avro.generic.{GenericRecord, GenericRecordBuilder}
import org.apache.avro.SchemaBuilder
import scala.util.{Failure, Success}

object HelloKryo {
  def main(args: Array[String]) {
    // Build a schema

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#!/bin/bash
pid=$1
nsamples=$2
sleeptime=$3

for x in $(seq 1 $nsamples)
  do
    jstack $pid
    sleep $sleeptime
  done | \

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type sample = {
  x : float;
  y : float
}

type model = {
  theta : float;
  beta  : float
}

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import xmlrpclib
from pprint import pprint
"""
A simple workout for the SoftLayer API as exposed via XML-RPC
"""
# TODO: Make this object-based instead of dictionary-based
# TODO: Read authentication information from a secure location
# TODO: Demonstrate how to call a method that requires a parameter
 
# Get this information from https://manage.softlayer.com/Administrative/apiKeychain

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import xmlrpclib
"""                                                                                                                                                                                                      
A simple Python wrapper for the SoftLayer API as exposed via XML-RPC                                                                                                                                     
"""
# TODO: Make this object-based for services, data types, and methods instead of dictionary-based                                                                                                         
# TODO: Read authentication information from a secure location                                                                                                                                           
# TODO: Demonstrate how to call a method that requires a parameter                                                                                                                           

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$ ./bin/start-hbase.sh 
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/hadoop/hbase/HBaseConfTool
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hbase.HBaseConfTool
	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:315)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:330)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:250)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:398)

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$ bin/hadoop org.apache.hadoop.hbase.PerformanceEvaluation sequentialWrite 4
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:zookeeper.version=3.3.1-942149, built on 05/07/2010 17:14 GMT
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:host.name=172.28.172.2
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:java.version=1.6.0_17
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:java.vendor=Apple Inc.
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:java.home=/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
10/06/11 03:29:15 INFO zookeeper.ZooKeeper: Client environment:java.class.path=/Users/hammer/codebox/hadoop-0.20.2+228/bin/../conf:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/tools.jar:/Users/hammer/codebox/hadoop-0.20.2+228/bin/..:/Users/hammer/codebox/hadoop-0.20.2+228/bin/../hadoop-0.20.2+228-core.jar:/Users/hammer/codebox/hadoop-0.20.2+228/bin/../lib/commons-cli-1.2.jar:/Users/hammer/codebox/hadoo

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import h5py

# HDF5 file with two arrays: 'trainxdata' (samples) and 'traindata' (labels)
INFILE_SAMPLES = ''
INFILE_REFERENCE_FASTA = ''
OUTFILE_FASTA = 'deepsea_train10k.fa'
OUTFILE_BED = 'deepsea_train10k.bed'

def onehot2base(onehot):
  if onehot == [1,0,0,0]:

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# deconstructSigs signatures.cosmic
library("deconstructSigs")
library("tibble")
signatures.cosmic.tidy <- tibble::rownames_to_column(as.data.frame(t(signatures.cosmic)))

# COSMIC http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
cosmic.current <- read.delim("http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt", check.names = F)
cosmic.current.clean <- cosmic.current[ , colnames(cosmic.current) != ""]
cosmic.current.tidy <- cosmic.current.clean[,names(cosmic.current.clean) not in c("Substitution Type","Trinucleotide")]

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FROM ubuntu:17.10

ENV LANG C.UTF-8

RUN apt-get update && \
    apt-get install -y python3 python3-pip libxml2-dev zlib1g-dev wget git cmake && \
    apt-get clean

RUN apt-get install -y python3-numpy # not necessary in scanpy 0.2.9.2/0.2.10