snakemake, singularity, and HPC

Posted on Mon 01 August 2022 in posts • Tagged with hpc, python, reproducibility

This is a bit of a sequel to my post last May about using conda environments with snakemake on the HPC. That solution worked for me, but was hacky and limited. This post will describe a different solution, which uses a singularity container containing a conda environment that can be …

Continue reading

Scripting figure creation with inkscape and python

Posted on Sat 06 November 2021 in posts • Tagged with python, science

I spent some time figuring out how to use inkscape and python to script the creation of figures that contain bitmaps, allowing for the user to specify the DPI when embedded. Normally, the way to handle this involves creating the figures directly in a vector graphics editor like inkscape or …

Continue reading

conda, snakemake, and HPC

Posted on Wed 05 May 2021 in posts • Tagged with hpc

NOTE: I have since come up with a solution that I like better / think is less hacky, described in this post.

NYU's new high performance computing (HPC) cluster, Greene, was put into production earlier this year and, on the new system, they want all users to use singularity containers for …

Continue reading

VSS 2020 project

Posted on Fri 19 June 2020 in posts • Tagged with science


In this post, I'm going to attempt to explain my poster at the Virtual Vision Sciences Society (VSS) conference, 2020, which starts today. The poster itself, along with a video walkthrough, an approximate transcript of that video, and some supplementary images, can be found on an OSF page (view …

Continue reading

Emacs python setup

Posted on Tue 01 January 2019 in posts • Tagged with emacs

I got a new laptop recently and so set up Emacs on it for the first time. Since my emacs init.el file has gotten progressively messier over the past several years, I took the opportunity to think about the variety of python packages I use and set things up …

Continue reading