adkinsrs

{
   "formatVersion" : 1,
   "tracks" : [
      {
         "type" : "SequenceTrack",
         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
         "label" : "DNA",
         "category" : "A Reference genome sequence",
         "key" : "Reference sequence",
         "urlTemplate" : "seq/chr22_with_ERCC92.fa",

adkinsrs

### BAM

# make a section for the new track called tracks.(unique name)
[ tracks.HBR1 ]

# settings for what data is shown in the track
# Symlinked /data/bam to /jbrowse/data/bam
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/HBR_1.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/HBR_1.accepted_hits.sorted_by_position.bam.bai

adkinsrs

rabbitmqctl list_queues name exclusive messages_ready messages_unacknowledged consumers state

rabbitmqctl list_connection

rabbitmqctl trace_on / trace_off
NOTE: f you turn trace_on then you can get a ‘firehose’ queue that shows all queue activity. 
In conjunction with knowing the IP addresses of the different nodes that was pretty handy in seeing what messages were going where.
Will need a seperate script (like in Python) to connect and dump it all.

adkinsrs

version: '2'
services:

  ergatis:
    image: adkinsrs/lgtseek
    links:
      - mongo
    mem_limit: 5120000000
    ports:
      - "8080:80"

adkinsrs

#! /usr/bin/perl

# BracketPicker.pl - will use to pick a bracket.  Better seeds get better odds of being picked
# This script has increasingly been adjusted to match the NCAA tournament format
# Shaun Adkins

use strict;
use warnings;
use POSIX;

adkinsrs

# This is the main Apache server configuration file.  It contains the
# configuration directives that give the server its instructions.
# See http://httpd.apache.org/docs/2.4/ for detailed information about
# the directives and /usr/share/doc/apache2/README.Debian about Debian specific
# hints.
#
#
# Summary of how the Apache 2 configuration works in Debian:
# The Apache 2 web server configuration in Debian is quite different to
# upstream's suggested way to configure the web server. This is because Debian's

adkinsrs

# This is the "Manatee" configuration file.
# This is a standard configuration file in which standard commenting rules apply.
#

# Database server options.  
# This setting is critical for Manatee to operate properly.  
#
# The format is SCHEMA:MYSQL:MYSQL_SERVER
# SCHEMA = Chado (DO NOT CHANGE)
# MYSQL = Using MySQL as the database vendor (DO NOT CHANGE)

adkinsrs

# Example MySQL config file for large systems.
#
# This is for a large system with memory = 512M where the system runs mainly
# MySQL.
#
# MySQL programs look for option files in a set of
# locations which depend on the deployment platform.
# You can copy this option file to one of those
# locations. For information about these locations, see:
# http://dev.mysql.com/doc/mysql/en/option-files.html