jerowe

jerowe

FROM continuumio/miniconda3:4.5.11

RUN apt-get update -y; apt-get upgrade -y; \
    apt-get install -y vim-tiny vim-athena ssh \
    build-essential gcc gfortran g++

# Always save your environments in a conda env file. 
# This makes it so much easier to fix your environment when you inadvertantly clobber it
# COPY (Relative to project) (/root)

jerowe

#!/usr/bin/env Rscript

# This example comes from the r-shiny examples github repo.
# https://github.com/rstudio/shiny-examples/blob/master/001-hello/app.R

library(shiny)



# Define UI for app that draws a histogram ----

jerowe

#!/usr/bin/env bash

### EasyBuild Installation and Module Deployment

##################################################################
## Make lmod available
##################################################################

source /usr/share/lmod/lmod/init/bash

jerowe

#!/usr/bin/env python

"""
Create Easybuild configs from conda packages

Create an EasyBuild Config for a Single Conda Package:

1. You can create an easybuild config using the anaconda client show syntax. If you do not specify a version the latest will be pulled in for you.

    python ./create_eb_configs_from_conda_packages.py module -p bioconda/samtools/1.9 bioconda/trimmomatic/0.39 bioconda/fastqc

jerowe

# run: conda env create -f environment.yml
# run: conda env update -f environment.yml
# run: conda env remove -n cellprofiler
# This installs the v3.18 version of cellprofiler, which at the time of writing is the most recent stable release
name: cellprofiler
# in order of priority: highest (top) to lowest (bottom)
channels:
  - anaconda
  - goodman # mysql-python for mac
  - bioconda

jerowe

FROM continuumio/miniconda3:4.5.11

RUN apt-get update -y; apt-get upgrade -y
RUN apt-get install -y vim-tiny vim-athena ssh openssh-server mysql-client default-libmysqlclient-dev openjdk-8-jdk build-essential

RUN mkdir -p /home/cellprofiler/cellprofiler
RUN mkdir -p /home/cellprofiler/.ssh
WORKDIR /home/cellprofiler

COPY environment.yml environment.yml

jerowe

from airflow import DAG
from icecream_sunday_dag_def import default_args
from icecream_sundae_linear_dag_def import generate_choose_cone_op, generate_choose_toppings_op, \
    generate_choose_icecream_flavor_op, generate_make_icecream_sundae_op

icecream_sundae_gather_dag = DAG('ice_cream_sundae_gather_dag', default_args=default_args, schedule_interval=None)

choose_cone_op = generate_choose_cone_op(icecream_sundae_gather_dag, 1)
choose_icecream_flavor_op = generate_choose_icecream_flavor_op(icecream_sundae_gather_dag, 1)
choose_toppings_op = generate_choose_toppings_op(icecream_sundae_gather_dag, 1)

jerowe

from airflow import DAG
from datetime import datetime, timedelta
from airflow.operators.python_operator import PythonOperator
import random
from pprint import pprint
from icecream_sunday_dag_def import choose_icecream_flavor, choose_cone, choose_toppings, make_icecream_sundae, \
    default_args

icecream_sundae_linear_dag = DAG('ice_cream_sundae_linear', default_args=default_args, schedule_interval=None)

jerowe

from airflow import DAG
from datetime import datetime, timedelta
from airflow.operators.python_operator import PythonOperator
import random
from pprint import pprint

default_args = {
    'owner': 'airflow',
    'depends_on_past': False,
    'start_date': datetime(2019, 1, 1),