ChristinaLK

import readin
import sys

if len(sys.argv) < 2:
  print "No Input"
else: 
	s = readin.readDataFromFile(sys.argv[1])
	out_dict = {"A":0,"T":0,"C":0,"G":0}
	for i in "ATCG":
    		out_dict[i] = s.count(i)

ChristinaLK

import readin
import sys

if len(sys.argv) < 2:
  print "No Input"
elif len(sys.argv) < 3:
	print "No Output"
else: 
	t = readin.readDataFromFile(sys.argv[1])
	#print t

ChristinaLK

import sys

def lineTest(tabl,ind,num):
    switch = True
    for i in tabl[ind]:
        if i > num:
            switch = False
            break
    return switch

ChristinaLK

library(dplyr)

# create empty dataframe
df <- data.frame(Domain=character(),
                 Total=integer(), 
                 Date=character()) 
# loop thru data files + add to data frame
for (date in c('2012-2013','2014-2015','2016-2017')) {
  # set data file path + read in data
  data <- load_data(date=date, time=365)

ChristinaLK

FROM python:3.6-stretch

COPY Miniconda3-latest-Linux-x86_64.sh /tmp

RUN mkdir /home/qiimeuser
ENV HOME /home/qiimeuser

RUN cd /tmp && \
    ./Miniconda3-latest-Linux-x86_64.sh -b -p /home/qiimeuser/miniconda3 && \
    export PATH=/home/qiimeuser/miniconda3/bin:$PATH && \

ChristinaLK

#!/bin/bash

img=$1
exec=$2
shift 2
args=$*

singularity exec -B $_CONDOR_SCRATCH_DIR:/scratch $img /scratch/$exec $args

ChristinaLK

#!/bin/bash

img=$1
exec=$2
shift 2
args=$*

cp /mnt/gluster/username/$img ./

singularity exec -B $_CONDOR_SCRATCH_DIR:/scratch $img /scratch/$exec $args

ChristinaLK

## use: 
## Rscript args.R 1 hello TRUE

values <- commandArgs(trailingOnly=TRUE)
print(values)

jobnumber <- values[1]
print(jobnumber) 

# if you want to use jobnumber as a NUMBER, not a STRING

ChristinaLK

#!/bin/bash
# this script is meant to be run on hpclogin2.chtc.wisc.edu
# it assumes that the gromacs-2022.tar.gz file has been downloaded to /software/smunawar
# To run the script, run the following command: 
# bash install.sh

# move to local disk for the compilation
mkdir /software/smunawar/gromacs
cd /scratch/local/smunawar
cp /software/smunawar/gromacs-2022.tar.gz ./

ChristinaLK

executable = run_python.sh
arguments = $(cw) $(hfiii) $(hfii) $(hfi) $(l)

transfer_output_remaps = "$(cow)_$(heiferIII)_$(heiferII)_$(heiferI)_$(calf).tar.gz=$(cow)/$(calf)/$(cow)_$(heiferIII)_$(heiferII)_$(heiferI)_$(calf).tar.gz"

queue cw,hfiii,hfii,hfi,l from csv

------
#!/bin/bash