ChristinaLK

import pandas as pd

## data was downloaded from XDMod, the Jobs by User dashboard

datafile = "Jobs__by_User_2024-10-01_to_2024-10-31_aggregate.csv"
outfile = "Jobs__by_User_2024-10-01_to_2024-10-31_subset.csv"

## build a dictionary with all the data

# needed conditionals to control flow

ChristinaLK

#!/bin/bash

type=$1
num=$2
datafile=$3

$type -n $num $datafile > $datafile.sub
[christina.koch@ap40 automation]$ cat simple.def 
Bootstrap: docker
From: hub.opensciencegrid.org/htc/rocky:9

ChristinaLK

library(palmerpenguins)
library(dplyr)
library(readr)

penguins %>% 
  filter(species == "Chinstrap") %>%
  select(island, body_mass_g, year) %>%
  group_by(island, year) %>%
  summarize(avg_body_mass_g = mean(body_mass_g)) %>%
  write_csv("chinstrap_avg_weights.csv")

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

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

## 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

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

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

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

ChristinaLK

#!/bin/bash

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

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

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

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)