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

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

#!/bin/bash

# Suggested by Github actions to be strict
# Taken from https://www.github.com/vsoch/pull-request-action
set -e
set -o pipefail

################################################################################
# Global Variables (we can't use GITHUB_ prefix)
################################################################################

vsoch

#!/bin/bash

BUCKET="${1}"
BLOB="${2}"
JOBSCRIPT="${3}"

mkdir -p /workdir 
cd /workdir
echo "bucket: $BUCKET"
echo "blob: $BLOB"

vsoch

#!/usr/bin/env python

import argparse
import datetime

from google.cloud import storage

def download_blob(bucket_name, source_blob_name, destination_file_name):
    """Downloads a blob from the bucket."""
    storage_client = storage.Client()

vsoch

#!/bin/bash

output=/media/$USER/My\ Passport/vubuntu/
if [ ! -d "$output" ]; then
   echo "$output not found, is drive connected to computer?"
   exit 1
fi

for folder in "Personal" "Transcripts" "Resume"; do
    rsync -avzh /home/$USER/Documents/$folder $output

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)

vsoch

FROM YOURCONTAINERHERE
# docker run --rm -it aquasec/microscanner --register <email address>
# docker build -t dirty-container .
RUN apk add --no-cache ca-certificates && update-ca-certificates
ADD https://get.aquasec.com/microscanner .
RUN chmod +x microscanner
RUN ./microscanner YOURTOKENHERE

vsoch

Apache with Singularity

Start with this recipe

Bootstrap: docker
From:httpd:2.4.37
%startscript
httpd-foreground