brentp

sudo apt-get install libtool
git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa dnaa-git
cd dnaa-git
# bfast required. see above gist
cp -r ../bfast-git ./bfast
# samtools require. see above gist.
cp -r ../samtools-svn/ ./samtools

sh autogen.sh && ./configure && make && sudo make install

sritchie

;; ## Example of timeseries aggregation in cascalog.
;; 
;; (copy paste all of this in at the REPL!)

(use 'cascalog.api)

(def tseries [["ndvi" 1 0 [1 2 3 4]]
              ["ndvi" 1 2 [2 3 4 5]]
              ["ndvi" 1 1 [4 3 2 1]]
              ["ndvi" 1 4 [1 2 3 4]]

cloudartisan

(ns staging.core
  (:require 
    [pallet.core :as core]
    [pallet.compute :as compute]
    [pallet.resource :as resource]
    [pallet.stevedore :as stevedore]
    [pallet.crate.automated-admin-user :as automated-admin-user]
    [staging.crate.mongodb :as mongodb]))

(def ec2-service

hugoduncan

{:debian-6-0-1-tb {:description "Debian Squeeze 6.0.1"
                   :os-family :debian
                   :os-version "6.0.1"
                   :os-type-id "Debian_64"
                   :os-64-bit true
                   :username "vmfest"
                   :password "vmfest"
                   :sudo-password "vmfest"}}

jnhutchinson

### KNITR SETUP

```{r setup, echo=FALSE}
opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE,  error=FALSE, message=FALSE, fig.height=11, fig.width=11)
```

### EXAMPLE CHUNK
```{r libraries}
library(ggplot2)
library(xtable)

jmchilton

import javax.net.ssl.HostnameVerifier;
import javax.net.ssl.SSLContext;
import javax.net.ssl.SSLSession;

import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
import com.sun.jersey.api.json.JSONConfiguration;
import com.sun.jersey.client.urlconnection.HTTPSProperties;

...

vsbuffalo

#!/bin/bash
# trim.sh - generic, slightly insane paired end quality trimming script
# Vince Buffalo <vsbuffaloAAAAAA@gmail.com> (sans poly-A)
set -e
set -u

## pre-config
ADAPTERS=illumina_adapters.fa
SAMPLE_NAME=some_sample_name
IN1=in1.fastq

arq5x

############################################################
# Novoalign
############################################################
export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa.novo.k14.s1.idx
export IRCHOME=/net/midtier18/vol79/cphg-quinlan2/projects/irradiated-clones
export STEPNAME=ircnovo
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=32000m:ncpus=16 -N $STEPNAME -m bea -M arq5x@virginia.edu";

echo "cd $IRCHOME; novoalign -d $GENOME -o SAM $'@RG\tID:parental\tSM:parental' -r Random \
             -f fastq/CgmW_AGTCAA_L001_R1.fastq.gz fastq/CgmW_AGTCAA_L001_R2.fastq.gz \

thickey

(ns pom2proj
  (:require [clojure.xml :as xml]
            [clojure.zip :as zip]
            [clojure.java.io :as io]
            [clojure.data.zip.xml :as zx])
  (:use [clojure.pprint :only [pprint]]))

(defn- text-attrs
  [loc ks]
  (map (fn [k]

brantfaircloth

Calling SNPs with GATK in non-model taxa

These notes build from several excellent sources:

• http://sfg.stanford.edu/
• http://www.broadinstitute.org/gatk/guide/
• http://www.broadinstitute.org/gatk/guide/topic?name=best-practices

and assume you're working with GATK 2.2-16. These notes also assume