vsoch

# This is a small script (that typically I copy paste) on a Google Cloud instance
# to set up an environment to mimic a worker. It includes installing snakemake,
# retrieving a package with the working directory (which typically has the 
# version of snakemake I aim to develop or debug, and then interactively debugging
# or doing this.

sudo apt-get install -y wget bzip2 ca-certificates gnupg2 git
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sudo chown -R $USER /opt
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 

vsoch

<?php
header('Content-type: text/xml');
/*
	Runs from a directory containing files to provide an
	RSS 2.0 feed that contains the list and modification times for all the
	files.

*/
$feedName = "My Audio Feed";
$feedDesc = "Feed for the my audio files in some server folder";

vsoch

% Multidimensional scaling (MDS) Example

% Load matlab cities data
load cities

% This data has cities in rows, and different categories for ratings in
% columns.  We will implement MDS to assess city similarity based on
% ratings.

% Step 1: Set up our proximity matrix

vsoch

Bootstrap: docker
From: ubuntu:16.04

%runscript
    . /torch/install/bin/torch-activate
    exec /bin/bash


%labels
MAINTAINER vsochat@stanford.edu

vsoch

#!/usr/bin/env python

# This is a helper script for the Google Life Sciences instance to be able to:
# 1. download a blob from storage, which is required at the onset of the Snakemake
#     gls.py download <bucket> <source> <destination>
# workflow step to obtain the working directory. 
# 2. Upload logs back to storage (or some specified directory of files)
#    gls.py save <bucket> <source-dir> <destination-dir>
#    gls.py save <bucket> /google/logs/output source/logs

vsoch

FROM ubuntu:16.04
LABEL version="1.0"

ENTRYPOINT [ "/singularity" ]

RUN mkdir -p /APPS /PROFILES
RUN chmod 0777 /APPS /PROFILES
RUN dpkg --add-architecture i386
RUN apt-get update && apt-get -y install wget less vim software-properties-common python3-software-properties apt-transport-https winbind
RUN wget https://dl.winehq.org/wine-builds/Release.key

vsoch

From:rocker/ropensci
Bootstrap:docker

%environment
PATH=$PATH:/opt/anaconda3/bin
export PATH

%runscript
Rscript /code/runman.R

vsoch

from sklearn.externals import joblib
import time
import numpy
import pickle

bigarray = numpy.zeros([190,91,190])
bigarray = bigarray.flatten()


### Saving

vsoch

Airflow Feedback

This is feedback about contribution to Apache Airflow.

Background

I first opened up a pull request in early March 2019 to add a Singularity operator to airflow. I am fairly experienced with Singularity (but not Airflow) so largely my strategy was to use an existing operator (Docker) as an example, and go from there. The interaction felt more controlled than usual because I was required to open a JIRA issue, but this wasn't terrible and is understandable for a larger community. A reviewer was very quick

vsoch

nu v0.3.0 (/home/vanessa/Documents/Dropbox/Code/rust/nushell-debian/nushell-0.3.0)
├── ansi_term v0.12.1 (in debian)
├── app_dirs v1.2.1
│   ├── ole32-sys v0.2.0
│   │   ├── winapi v0.2.8 (outdated)
│   │   └── winapi-build v0.1.1 (in debian)
│   ├── shell32-sys v0.1.2
│   │   ├── winapi v0.2.8 (outdated)
│   │   └── winapi-build v0.1.1 (in debian)
│   ├── winapi v0.2.8 (outdated)