carlcrott

Code changes should only be pushed to github if all tests are green.


Below is a common work-flow for a team working with a central repo. several variations are possible, but if unsure, please go by this:

   1. if you are working from a Pivotal Tracker story, click "start" on that story
   2. git pull (or, if this is your first time ever getting the code, do git clone git@github.com:our_repo/our_repo.git to get a local copy of the repo)
   3. rake db:migrate
   4. rake db:test:prepare
   5. spec spec

carlcrott

RVM .bashrc
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples
# If not running interactively, don't do anything
if [[ -n "$PS1" ]]; then
        # don't put duplicate lines in the history. See bash(1) for more options
        # ... or force ignoredups and ignorespace
        HISTCONTROL=ignoredups:ignorespace
        # append to the history file, don't overwrite it

carlcrott

////////////////////////////The Error //////////////////////////////

unf-ubu@unf-ubu:~/rails_projects/crossbow$ ruby EMR_job.rb
http://crossbow-refs.s3.amazonaws.com/hg18.jar

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    An unexpected error has occurred.
  Please report the following lines to:
   s3tools-bugs@lists.sourceforge.net
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

carlcrott

$./cb_emr \
    --name "Crossbow-HG18" \
    --preprocess \
    --input=s3n://bg-crossbow-01/example/human_g18/small.manifest \
    --output=s3n://bg-crossbow-01/example/human_g18/output_full \
    --reference=s3n://bg-crossbow-01/crossbow-refs/hg18.jar \
    --instances 1

carlcrott

from django.db import models

class Gene(models.Model):
    sequence = models.CharField(max_length=500)
    chromosome = models.CharField(max_length=10)

carlcrott

## Java

Oscar oscar = new Oscar();
List<ResolvedNamedEntity> entities = oscar.findAndResolveNamedEntities(s);
for (ResolvedNamedEntity ne : entities) {
    System.out.println(ne.getSurface());
    ChemicalStructure inchi = ne.getFirstChemicalStructure(FormatType.INCHI);
    if (inchi != null) {
        System.out.println(inchi);
    }

carlcrott

thrive@thrive-laptop:~/rails_projects/sinatra-jruby-heroku$ git push heroku master
Counting objects: 7, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 646 bytes, done.
Total 6 (delta 3), reused 0 (delta 0)

-----> Heroku receiving push
-----> Java app detected
-----> Installing Maven 3.0.3..... done

carlcrott

# Example

1. Install Jruby ( I'm using RVM, which makes it painfully easy )

2. Trial
<pre>
$ rvm install jruby
$ rvm use jruby
</pre>

carlcrott

# composed of code from: 
# http://whatcodecraves.com/articles/2008/02/05/setup_rails_with_postgresql/
# http://www.tokumine.com/2009/09/03/jruby-postgres-rails/

common: &common
  adapter: jdbcpostgresql
  username: oscar
  password: XXXXX
  host: 127.0.0.1
  port: 5432

carlcrott

<project>
	<modelVersion>4.0.0</modelVersion>
	<groupId>net.chowie</groupId>
	<artifactId>jruby-heroku</artifactId>
	<version>1.0</version>
	<name>sinatra-jruby-heroku</name>
	<packaging>jar</packaging>
	<dependencies>
		<dependency>
			<groupId>org.jruby</groupId>