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@martijnvermaat
martijnvermaat / gonl_freqs.py
Created Oct 22, 2015
CSV with allele frequencies from GoNL VCF
View gonl_freqs.py
#!/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
@martijnvermaat
martijnvermaat / README.md
Last active Apr 29, 2016
Vagrant configurations
View README.md

Default Vagrant configurations.

Application IP SSH forward HTTP forward HTTPS forward
Mutalyzer 192.168.111.222 2522 8088 8089
Base server 192.168.111.223 2523
Varda 192.168.111.224 2524 8090 8091
ELK 192.168.111.225 2525 8092 8093
logstash-forwarder 192.168.111.226 2526
Jenkins 192.168.111.227 2527 8094
@martijnvermaat
martijnvermaat / gencert.sh
Last active Jul 17, 2018
Generate self-signed x509 certificates
View gencert.sh
#!/bin/bash
# Generate a self-signed x509 certificate or certificate signing request and
# key using OpenSSL. DNS and IP addresses can be added as subjectAltName
# entries.
#
# Usage:
# ./gencert.sh <common name (or DNS name)> <DNS names or ip addresses...> [--rsa4096] [--csr]
#
# By default, a 2048 bits RSA key is generated. Supply --rsa4096 at the end to
# generate a 4096 bits key.
@martijnvermaat
martijnvermaat / app.jsx
Last active Aug 29, 2015
plexus-form #31
View app.jsx
'use strict';
var React = require('react');
var Form = require('plexus-form');
var Example = React.createClass({
getInitialState: function() {
return {values: {name: 'Pierre'}};
},
onSubmit: function(output, value, errors) {
@martijnvermaat
martijnvermaat / plink_dbsnp.md
Last active May 30, 2016
Rename Plink SNPs to their dbSNP rs#
View plink_dbsnp.md
View emacs.md

Emacs notes

Just some Emacs things that I cannot seem to remember without writing them down. I'm an Emacs newbie (but have been using it for 15 years).

These are random and specific to my setup, so probably not useful to anyone else.

Config can be found here: https://github.com/martijnvermaat/dotfiles

@martijnvermaat
martijnvermaat / windows_batch_checker.md
Created Jan 30, 2015
Running the automated Batch Checker
View windows_batch_checker.md

Running the automated Batch Checker

(By Jeroen Laros.)

Installation

Python core libraries

Go to the Python website. In the Downloads tab, click the Python 2.7.9

@martijnvermaat
martijnvermaat / .gitignore
Last active Aug 29, 2015
Profiling k-mer pairwise comparison
View .gitignore
.ipynb_checkpoints
*.pdf
*.fa
[abcde].k1
[abcde].k2
[abcde].k3
[abcde].k4
[abcde].k5
[abcde].k6
[abcde].k7
@martijnvermaat
martijnvermaat / limit-directory-size
Created Sep 6, 2014
Limit directory size by deleting files accessed least recently
View limit-directory-size
#!/bin/bash
# Limit directory size by deleting files accessed least recently.
#
# Use inotify to wait for files written to the specified directory. On such an
# event, and if the directory size is over the specified maximum size, keep
# deleting files until the size is below the maximum. Repeat (so, never exit).
#
# Names of deleted files are written to stdout, messages are prefixed with the
# string ">>>".
#
@martijnvermaat
martijnvermaat / fix_sslv3.sh
Last active Jan 5, 2016
Fix curl/gnutls SSLv3 on Ubuntu 14.04
View fix_sslv3.sh
#!/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
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