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martijnvermaat / manual.md
Created April 18, 2016 09:07
Nested Manual

Quick introduction

Initial screen

When the program is started, the user is presented with a minimal pedigree consisting of a father, a mother and a child. On the left of the screen there is a slider for zooming in and zooming out.

In the top left corner three buttons can be seen, two of them (undo and redo) are greyed out. The third button is for downloading the pedigree.

In the top right corner two buttons can be seen, the left one (drawing view) is

@martijnvermaat
martijnvermaat / index.html
Created February 29, 2016 16:12
Merge rules with vendor-specific pseudo-element selectors
<!doctype html>
<style>
#original input[type=range] {
-webkit-appearance: none !important;
}
#original input[type=range]::-webkit-slider-runnable-track {
height: 2px;
width: 100px;
background: red;
@martijnvermaat
martijnvermaat / fix_sslv3.sh
Last active January 5, 2016 10:07
Fix curl/gnutls SSLv3 on Ubuntu 14.04
#!/bin/bash
# Fix curl/gnutls SSLv3 on Ubuntu 14.04
#
# The curl version on Ubuntu 14.04 Trusty Tahr has a bug (through gnutls) in
# its SSLv3 support. This also affects git.
#
# http://sourceforge.net/p/curl/bugs/1319/
#
# This downgrades curl to 7.32 (from Ubuntu 13.12), which does not have the
# bug. It also uninstalls the landscape-client and python-pycurl packages
@martijnvermaat
martijnvermaat / profiling.ipynb
Last active December 30, 2015 00:29
Profiling k-mer pairwise comparison
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martijnvermaat / .gitignore
Last active December 21, 2015 06:48
Benchmark: CyVCF versus PyVCF
*.vcf.gz
@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 / 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 / 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:
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martijnvermaat / mutalyzer-webservice.ipynb
Created February 26, 2013 14:14
Using the Mutalyzer webservice
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martijnvermaat / gonl_freqs.py
Created October 22, 2015 14:09
CSV with allele frequencies from GoNL VCF
#!/usr/bin/env python
#
# CSV with allele frequencies from GoNL VCF.
#
# https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/
import sys
from vcf import Reader