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martijnvermaat / userContent.css
Last active August 29, 2015 14:03
Hide comments on Losse Veter (losseveter.nl)
/*
* Hide comments on Losse Veter (losseveter.nl)
*
* Most of the user comments on Losse Veter are either racist or zealot
* epistels about doping. With this Firefox setting, you can enjoy just
* the track and field news.
*
* Edit this file and copy it as userContent.css into your Firefox
* profile-directory/chrome/
*/
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martijnvermaat / __init__.py
Last active July 20, 2018 14:37
Matplotlib for use in LaTeX
import math
from matplotlib import rcParams
def configure(document_fontsize=14.4, available_width=307.28987):
"""
Configures Matplotlib so saved figures can be used in LaTeX documents.
Uses the sans-serif TeX Gyre Heros font (Helvetica), also for math.
@martijnvermaat
martijnvermaat / logo.ipynb
Last active August 29, 2015 13:56
kMer logo
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martijnvermaat / example.png
Last active August 29, 2015 13:56
Overlap-relative centers
example.png
@martijnvermaat
martijnvermaat / ssh-agent-forwarding-screen.md
Created December 21, 2013 15:06
SSH agent forwarding and screen

SSH agent forwarding and screen

When connecting to a remote server via SSH it is often convenient to use SSH agent forwarding so that you don't need a separate keypair on that server for connecting to further servers.

This is enabled by adding the

ForwardAgent yes

option to any of your Host entries in ~/.ssh/config (or alternatively with the -A option). Don't set this option in a wildcard Host * section since any user on the remote server that can bypass file permissions can now als use keys loaded in your SSH agent. So only use this with hosts you trust.

@martijnvermaat
martijnvermaat / raspberry-pi-config.md
Last active February 3, 2023 01:53
Notes on my Raspberry Pi server config

Notes on my Raspberry Pi server config

This describes how I installed and configured my Raspberry Pi model B (512MB).

The Pi is mainly used as SSH jump host, IRC client, Git server, backup fileserver, etc. It doesn't need stellar performance, it just has to be cheap, low in power usage, and secure.

Raspbian on encrypted root

@martijnvermaat
martijnvermaat / profiling.ipynb
Last active December 30, 2015 00:29
Profiling k-mer pairwise comparison
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martijnvermaat / gitlab-ipython-notebook.md
Last active May 8, 2023 00:53
View IPython notebooks in GitLab

Viewing IPython notebooks in GitLab

GitLab is open source software to collaborate on code (a GitHub clone to run on your own server). Clicking a blob (a file in a repository) in GitLab shows a nice rendering if GitLab supports the file type (e.g., images, Markdown documents), or its content as plain text otherwise. The patch described here adds support to GitLab for rendering IPython notebooks (.ipynb files).

@martijnvermaat
martijnvermaat / README.md
Last active February 7, 2022 09:06
The IPython Notebook on an SGE cluster

IPython Notebook on an SGE cluster

This guide documents how we set up an easy workflow for using the IPython Notebook on our compute cluster managed with Sun Grid Engine (SGE).

Summary: We provide a script to the cluster users that runs qrsh to schedule an ipython notebook job using SSL and password protection.

Installing IPython

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martijnvermaat / .gitignore
Last active December 21, 2015 06:48
Benchmark: CyVCF versus PyVCF
*.vcf.gz