mbreese

production:
    disable_default: true
    methods:
    - adapter: Gitorious::Authentication::LDAPAuthentication
      server: 10.1.?.?
      port: 389 
      base_dn: DC=domain,DC=org       
#      bind_username: binduser
#      bind_password: binduserpass
      user_filter: 

mbreese

Environmental Modules

Environment Modules is a utility that has been used to manage executables and paths for high-performance computing clusters for multiple decades (1991!). The basic idea is that you can use modules to adapt your processing environment (and $PATH) to make sure that your environment is consistent. Importantly, this allows system administrators the ability to install and maintain multiple versions of software for different users. This tool can also be used to effectively manage your bioinformatics processing pipelines to ensure consistent analysis runs. For example, if you have a set of samples that will need to be analyzed consistently over a long time span, you could use modules to make sure that the same version of a program is used throughout the entire experiment while letting you use newer versions for different experiments.

Installation

If you are running your samples on a computing cluster, chances are you are already using modules to configure your environment (add progra

mbreese

docker run  -v /Users/mbreese/tmp:/tmp1 -w /tmp1 -i centos:7 /bin/bash -s <<EOF 
date > foo
echo 'foo' >> foo
cat /etc/redhat-release >> foo
whoami >> foo
EOF

mbreese

#!/bin/bash
TARGETDIR=$1
if [ "$TARGETDIR" = "" ]; then
TARGETDIR=$(python -c 'import os; print os.path.realpath("local")')
fi
mkdir -p $TARGETDIR

libevent() {
  curl -LO https://github.com/libevent/libevent/releases/download/release-2.0.22-stable/libevent-2.0.22-stable.tar.gz
  tar -zxvf libevent-2.0.22-stable.tar.gz

mbreese

Keybase proof

I hereby claim:

• I am mbreese on github.
• I am mbreese (https://keybase.io/mbreese) on keybase.
• I have a public key ASCjOVAWFXFGWcm-XDsTCHs1XARvuKNQVDgozMYNNSPC9Ao

To claim this, I am signing this object:

mbreese

CREATE ROLE db_user LOGIN ENCRYPTED PASSWORD 'secret-password' NOSUPERUSER INHERIT NOCREATEDB NOCREATEROLE NOREPLICATION;
CREATE DATABASE db_name WITH OWNER db_user;
GRANT ALL PRIVILEGES ON DATABASE db_name TO db_user;

mbreese

#!/usr/bin/env python

import sys

prefix="VEP_"
vep_info_name = "CSQ"


def parse_info_format(line):
###INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|...">

mbreese

#!/usr/bin/env python

import sys
import itertools

cons_key = "VEP_Consequence"
impact_key = "VEP_IMPACT"
gene_key = "VEP_SYMBOL"
csn_key = "VEP_CSN"
sift_key = "VEP_SIFT"

mbreese

#!/usr/bin/env python

import sys
import datetime

rate = 100000

if len(sys.argv) > 1:
    rate = int(sys.argv[1])

mbreese

#!/bin/bash
# 
# This will by default take snapshots of all zfs filesystems, 
# but could be adapted to only pull specific ones. This script 
# will also rotate snapshots, removing those that are older 
# than 2 weeks.
#

CURDATE=$(date +%Y%m%d)
TWOWEEKSAGO=$(date -d'2 weeks ago' +%Y%m%d)