pditommaso

use strict;
use Bio::SeqIO;
my $in  = Bio::SeqIO->new(-file => "input.fa",-format => 'Fasta');

my $seq;
while ( $seq = $in->next_seq() ) {
 print $seq->display_id() . " - " .  $seq->seq() . "\n";
}

pditommaso

/* 
 * This is script for the Jenkins email-ext plugin.
 * It make it possibile to send a mail for failing downstream jobs to 
 * source committer. It have to be used for.
 *  
 * Usage: save this script in $JENKINS_HOME/email-templates/committers.groovy
 * In the job configuration use the value "${SCRIPT, script="committers.groovy"}"
 * in the field "Global Recipient List" for the component "Editable Email Notification"
 * 
 */ 

pditommaso

import java.io.*;

public class TestProcessIO {

  public static boolean isAlive(Process p) {
    try {
      p.exitValue();
      return false;
    }
    catch (IllegalThreadStateException e) {

pditommaso

#!/bin/sh
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
# NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

pditommaso

/**
 * Based on Stackoverflow answer http://stackoverflow.com/a/2729907/395921
 * 
 * @author Paolo Di Tommaso
 *
 */
public class Names {

	
	/**

pditommaso

#!/bin/bash

trap "echo You\'re trying to Control-z me" SIGTSTP
while :; do
:
done

pditommaso

import java.io.RandomAccessFile
import java.nio.channels.FileChannel
import org.jboss.netty.buffer.{ByteBufferBackedChannelBuffer, ChannelBuffer, ChannelBuffers}

/**
 * Maps a the filename to a memory mapped random access file across 1 or more buffers.
 * Support files up to Long.MAX_VALUE.
 *
 * @param filename the file to map
 * @param maxBufferSize the maximum number of bytes to map per buffer

pditommaso

#!/bin/env groovy
/*
 * Delete all the files which name ends with the suffix '_debug' except the most recent 10
 */

def cli = new CliBuilder(usage:'clean-folder.groovy [-d] <folder to clean>')
cli.d('delete old files')
def options = cli.parse(args)

if( options.arguments().size() != 1 ) {

pditommaso

#!/bin/bash
export AWS_ACCESS_KEY=omissis
export AWS_SECRET_KEY=omissis
export CIRCO_CLUSTER=circotest1
curl http://cbcrg-eu.s3.amazonaws.com/circo-cloud-bootstrap.sh | bash &> circo-boot.log

pditommaso

import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Stack;

/**
 * An example class for directed graphs.  The vertex type can be specified.