icaoberg

#!/bin/bash
#SBATCH -p gpu
#SBATCH -e tensorflow.%j.err 
#SBATCH -o tensorflow.%j.out
#SBATCH -t 48:00:00
#SBATCH -n 1
#SBATCH --mem=32G
#SBATCH --gres=gpu:1

#so we can use modules

icaoberg

#!/bin/bash

scontrol show jobid $1 | grep StdOut | cut -d"=" -f2  | xargs tail

icaoberg

from os import path
import os
from scipy.misc import imread
import matplotlib.pyplot as plt
import random

import urllib

from wordcloud import WordCloud, STOPWORDS

icaoberg

#!/usr/bin/python

from time import gmtime, strftime
today=strftime("%Y%m%d")
now=strftime("%H:%M:%S")
output_file = today + '.txt'
fid = open( output_file, 'a' )

#-----------------------------------------------------------------------
# twitter-trends

icaoberg

FILE=img1.tif

if [ -f $FILE ]; then
  echo "File "$FILE" exists."
else
  echo "File "$FILE" does not exist."
  exit -1
fi

icaoberg

addpath( 'OMERO.matlab-5.2.2-ice35-b17' )

server = 'localhost';
port = 4064;
username = 'murphylab';
password = 'murphylab';

client = loadOmero( server, port );
session = client.createSession( username, password );

icaoberg

digraph demo2D00_calls {                                                     
rankdir="LR"                                                                 
node [shape=box, color=blue]                                                 
   demo2D00 -> ml_initparam;                                                 
   demo2D00 -> slml2img;                                                     
   AdjustResolutions -> tp_stretch3d;                                        
   AverageEnergy -> est_curv;                                                
   CompressLib -> packableObject;                                            
   Greedy3D_integration_compressed -> Greedy3D_compressed_default_options;   
   Greedy3D_integration_compressed -> Greedy3D_single_step_compressed;       

icaoberg

#!/bin/bash

##make virtual environment
virtualenv --system-site-packages .

##activate virtual environment
source ./bin/activate

#get biopython
pip install -U biopython

icaoberg

#!/bin/bash

##this is an example described in section 2.4.1
##http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc10

wget -nc http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.fasta

echo "
from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):

icaoberg

#!/bin/bash

## Ivan E. Cao-Berg (icaoberg@scs.cmu.edu)
## Copyright (C) 2016
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published
## by the Free Software Foundation; either version 2 of the License,
## or (at your option) any later version.
##