martijnvermaat

#!/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

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

#!/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

'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

Rename plink SNPs to their dbSNP rs id

Download a dbSNP database from the UCSC as a CSV file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

For example:

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp137Common.txt.gz

Note that the chromStart column values are 0-based.

martijnvermaat

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

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

.ipynb_checkpoints
*.pdf
*.fa
[abcde].k1
[abcde].k2
[abcde].k3
[abcde].k4
[abcde].k5
[abcde].k6
[abcde].k7

martijnvermaat

#!/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

#!/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