| % Mutual Information | |
| % This shows why mutual information is important for registration, more-so | |
| % than another metric like the least sum of squares. | |
| % VSoch July 2013 | |
| % First, let's read in two pickle images that we want to register | |
| % Note - this is a picture I found on google search, and I transformed it in | |
| % photoshop by moving it down and right, and then CONTROL+I to get the inverse | |
| pickle1 = imread('pickle1.png'); | |
| pickle2 = imread('pickle2.png'); |
| % clingo dinosaur.lp | |
| % These are blanket facts, statements that each of these is living | |
| % I think these are called atoms | |
| living(vanessa). | |
| living(fernando). | |
| living(maria). | |
| % This tells use size of arms for each living thing | |
| armsize(vanessa, "small"). | |
| armsize(fernando, "large"). |
| from sklearn.externals import joblib | |
| import time | |
| import numpy | |
| import pickle | |
| bigarray = numpy.zeros([190,91,190]) | |
| bigarray = bigarray.flatten() | |
| ### Saving |
| # 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 $USER /opt | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda |
| % Multidimensional scaling (MDS) Example | |
| % Load matlab cities data | |
| load cities | |
| % This data has cities in rows, and different categories for ratings in | |
| % columns. We will implement MDS to assess city similarity based on | |
| % ratings. | |
| % Step 1: Set up our proximity matrix |
| #!/usr/bin/env python | |
| # This is a helper script for the Google Life Sciences instance to be able to: | |
| # 1. download a blob from storage, which is required at the onset of the Snakemake | |
| # gls.py download <bucket> <source> <destination> | |
| # workflow step to obtain the working directory. | |
| # 2. Upload logs back to storage (or some specified directory of files) | |
| # gls.py save <bucket> <source-dir> <destination-dir> | |
| # gls.py save <bucket> /google/logs/output source/logs |
| FROM ubuntu:16.04 | |
| LABEL version="1.0" | |
| ENTRYPOINT [ "/singularity" ] | |
| RUN mkdir -p /APPS /PROFILES | |
| RUN chmod 0777 /APPS /PROFILES | |
| RUN dpkg --add-architecture i386 | |
| RUN apt-get update && apt-get -y install wget less vim software-properties-common python3-software-properties apt-transport-https winbind | |
| RUN wget https://dl.winehq.org/wine-builds/Release.key |
| From:rocker/ropensci | |
| Bootstrap:docker | |
| %environment | |
| PATH=$PATH:/opt/anaconda3/bin | |
| export PATH | |
| %runscript | |
| Rscript /code/runman.R |
This is feedback about contribution to Apache Airflow.
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
| 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) |