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martijnvermaat / mutalyzer-webservice.ipynb
Created February 26, 2013 14:14
Using the Mutalyzer webservice
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martijnvermaat / README.md
Last active December 19, 2015 12:29
IPython nbconvert to HTML and LaTeX escaping

Export to HTML with LaTeX

It looks like some escaping is not handled properly.

Steps to reproduce

  1. Open the notebook with IPython notebook and observe that all looks fine:
@martijnvermaat
martijnvermaat / README.md
Last active December 19, 2015 12:38
IPython nbconvert to reveal.js scrollbar

Export to reveal.js introduces a scrollbar

Exporting a notebook with one simple slide to reveal.js introduces a vertical scrollbar (but only if the browser window is wide enough, like over 800px).

This is on current IPython master and was not the case for older nbconvert versions, but I'm unsure which versions exactly.

I also have no clue what the problem is, it must have something to do with the reveal template.

@martijnvermaat
martijnvermaat / postmkvirtualenv
Last active December 20, 2015 09:49
Link PyGTK/Pycairo/PyQt/wxPython from system packages in virtual environment
#!/bin/bash
# This hook is run after a new virtualenv is activated.
#
# For use with virtualenvwrapper [1], based on [2].
#
# This script makes it possible to use PyGTK/Pycairo/PyQt/wxPython in Python
# virtual environments from the corresponding system packages. It is tested on
# Debian wheezy and Ubuntu 12.04.
#
# Copy this script to `~/.virtualenvs/postmkvirtualenv` (make it executable)
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martijnvermaat / .gitignore
Last active December 21, 2015 06:48
Benchmark: CyVCF versus PyVCF
*.vcf.gz
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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

@martijnvermaat
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 / profiling.ipynb
Last active December 30, 2015 00:29
Profiling k-mer pairwise comparison
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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

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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.