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### 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) |
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(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] |
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{: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"}} |
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(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 |
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;; ## 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]] |
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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 |
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