sahilseth

## ------ download this file:
## wget https://gist.githubusercontent.com/sahilseth/01d5e88e431334fcd527/raw -O cloud_formation.sh
## bash cloud_formation.sh

## run this file
## chmod u+x cloud_formation.sh

## Assuming you are running this as ubuntu user

### --------- Install from apt-get

sahilseth

#!/bin/sh
#----------------------------------------------------------------
# Daily Backup Routine - Backup and Sync to Dropbox
# This script creates a backup using today's date, then deleted
# any backups made 3 days ago. If run every day it will ensure
# you have a week's worth of backups of your MySQL databases and
# zPanel web directories. 
#
# Uses whatever Dropbox account is running on the server.
#

sahilseth

## a vector of full paths to fastq files (mate 1)
fqs1 = rep("myfile.fastq", 20)
## a vector of full paths to fastq files (mate 2)
fqs2 = rep("myfile.fastq", 20)
## full path to bwa
bwa_exe = ""
bwa_aln_opts = ""
bwa_sampe_opts = ""

sahilseth

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

sahilseth

## make a dir to install
sudo mkdir -m 775 /apps
chown sahilseth /apps

## download to a tmp space
cd /tmp
wget http://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz
tar -zxvf R-3.2.2.tar.gz
cd R-3.2.2
./configure --prefix /apps/R/3.2.2/ --enable-R-shlib --enable-R-profiling \

sahilseth

jobname	sub_type	prev_jobs	dep_type	queue	memory_reserved	walltime	cpu_reserved	platform	jobid
create_db	serial	none	none	short	2000	1:00	1	local	1
rna2dna1	serial	create_db	serial	short	2000	1:00	1	local	2
echorna1	serial	rna2dna1	serial	short	2000	1:00	1	local	3
rna2dna2	serial	create_db	serial	short	2000	1:00	1	local	4
echorna2	serial	rna2dna2	serial	short	2000	1:00	1	local	5
rna2dna3	serial	create_db	serial	short	2000	1:00	1	local	6
echorna3	serial	rna2dna3	serial	short	2000	1:00	1	local	7

sahilseth

mn=1;mx=10
pb <- txtProgressBar(mn, mx, style = 3)
tmp <- lapply(mn:mx, function(x){
	pb$up(x)
	Sys.sleep(0.5)
	#message("I am doing something...")
})

sahilseth

setwd("~/pub/slides/rmeetup_oct2015")

# get commands ------------------------------
hello='echo Hello World !'

sleep=c('sleep 5', 'sleep 5')

tmp=c('cat $RANDOM > tmp1', 
			'cat $RANDOM > tmp2')
			

sahilseth

df = data.frame(id = 1:10, fname = paste0("name", 1:10))

nms = c(id = "the unique id which does this or that",
        fname = "first name of a person")

attr(df, 'info') <- nms

## let is see how this looks
attr(df, "info")

sahilseth

## add this to bashrc:
export PYTHONPATH=$PYTHONPATH:~/lib/python2.7/site-packages/

module load Python
python setup.py install --prefix=$HOME