dyndna

#!/bin/bash
#
# Example of how to parse short/long options with 'getopt'
#

OPTS=`getopt -o vhns: --long verbose,dry-run,help,stack-size: -n 'parse-options' -- "$@"`

if [ $? != 0 ] ; then echo "Failed parsing options." >&2 ; exit 1 ; fi

echo "$OPTS"

dyndna

#### Parallel MPI BZIP2
## See man doc at http://compression.ca/mpibzip2/
### for .tar or tar.bz2 files,
## mpirun -np 4 mpibzip2 myfile.tar or  mpirun -np 4 mpibzip2 myfile.tar.bz2
### for tar.gz files, see pigz at http://serverfault.com/a/270825/149084
## pigz -dk -p 4 target.tar.gz | tar -xf
# remove -k to delete original file after decompression.

# Make file for MPI BZIP2
SHELL=/bin/sh

dyndna

'''
    This script will attempt to open your webbrowser,
    perform OAuth 2 authentication and print your access token.

    It depends on two libraries: oauth2client and gflags.

    To install dependencies from PyPI:

    $ pip install python-gflags oauth2client
    

dyndna

#### Get gene annotations ####
# By Michael Love, http://www.bioconductor.org/help/workflows/rnaseqGene/

library("AnnotationDbi")
library("org.Hs.eg.db")
columns(org.Hs.eg.db)

convertIDs <- function( ids, from, to, db, ifMultiple=c("putNA", "useFirst")) {
  stopifnot( inherits( db, "AnnotationDb" ) )
  ifMultiple <- match.arg( ifMultiple )

dyndna

Install kallisto on HPC

cd kallisto-0.42.5/build
cmake ..

-- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Check for working C compiler: /usr/bin/cc

dyndna

import urllib
import urllib2
import time
import json

#Credit: https://gist.github.com/jackcarter/d86808449f0d95060a40 and 
# https://gist.github.com/jackcarter/d86808449f0d95060a40#gistcomment-1755139

# put oauth test token between ''
token = ''