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vsoch /
Created Oct 20, 2020
Snakemake Debugging on Google Cloud
# 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
sudo chown -R $USER /opt
bash -b -p /opt/conda
vsoch / index.php
Last active Oct 19, 2020
Generate RSS feed for files in a directory folder. Put this file in a folder with files, modify the $allowed_ext variable to customize your extensions, and $feedName, $feedDesc, $feedURL, and $feedBaseURL. Then navigate to the folder on the web to see the xml feed. Done!
View index.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
$feedName = "My Audio Feed";
$feedDesc = "Feed for the my audio files in some server folder";
vsoch / vcademy_mds.m
Created Aug 6, 2013
Multidimensional Scaling: a simple Matlab demonstration
View vcademy_mds.m
% 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 / Singularity
Last active Sep 15, 2020
A quick tutorial on how to generate a Singularity image with loadcaffee
View Singularity
Bootstrap: docker
From: ubuntu:16.04
. /torch/install/bin/torch-activate
exec /bin/bash
vsoch /
Last active Sep 2, 2020
Testing Google Life Sciences updated download / upload script (will be put into version control)
#!/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
# download <bucket> <source> <destination>
# workflow step to obtain the working directory.
# 2. Upload logs back to storage (or some specified directory of files)
# save <bucket> <source-dir> <destination-dir>
# save <bucket> /google/logs/output source/logs
vsoch / Dockerfile
Last active Aug 25, 2020
Dolmades Files
View Dockerfile
FROM ubuntu:16.04
LABEL version="1.0"
ENTRYPOINT [ "/singularity" ]
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
vsoch / Singularity
Last active Aug 17, 2020
Singularity image with anaconda + R
View Singularity
export PATH
Rscript /code/runman.R
from sklearn.externals import joblib
import time
import numpy
import pickle
bigarray = numpy.zeros([190,91,190])
bigarray = bigarray.flatten()
### Saving
vsoch /
Last active Jan 22, 2020
Apache Airflow Feedback 1/22/2020

Airflow Feedback

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

vsoch / cargo-debstatus-nu-0.3.0_10-17-2019.txt
Last active Dec 7, 2019
nu 0.3.0 dependency output from running cargo-debstatus in the root of the repository, and commenting out #default-run = "nu" in Cargo.toml. Do a find for (outdated) to highlight all the packages that were highlighted in yellow on the terminal (that I cannot show here)
View cargo-debstatus-nu-0.3.0_10-17-2019.txt
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)
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