Skip to content

Instantly share code, notes, and snippets.

View brainstorm's full-sized avatar

Roman Valls Guimera brainstorm

267 followers · 810 following
View GitHub Profile
@brainstorm
brainstorm / Preferential attachment algorithm.ipynb
Last active August 29, 2015 14:00
Preferential attachment algorithm with Guido's graph notation
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@brainstorm
brainstorm / keybase.md
Last active August 29, 2015 14:01

Keybase proof

I hereby claim:

  • I am brainstorm on github.
  • I am brainstorm (https://keybase.io/brainstorm) on keybase.
  • I have a public key whose fingerprint is F12F E607 E080 588A F5CE D8F1 12A5 388F 08F8 0CB5

To claim this, I am signing this object:

@brainstorm
brainstorm / piperget.sh
Last active August 29, 2015 14:02
piperget.sh: Fetching pipermail gzipped archives and converting them to .mbox format
#!/bin/sh
# Usage: piperget.sh https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/
# automated retrieval of pipermail archives & conversion to mbox file
# Last edit: 2012/10/09 Tue 23:16 PDT
listname=$(echo "$1" | sed 's:^\(http.*\)/\([^/]*\)/$:\2:')
cd /tmp
wget -r -l 1 -nH -A *.txt.gz "$1"
touch /tmp/pipermail/$listname/$listname.mbox
chmod 600 /tmp/pipermail/$listname/$listname.mbox
cd /tmp/pipermail/$listname
@brainstorm
brainstorm / dataspace-kibana.json
Created June 25, 2014 15:20
DataSpace Kibana JSON definition
{
"title": "Logstash Search",
"services": {
"query": {
"list": {
"0": {
"query": "loglevel: ERROR",
"alias": "errors",
"color": "#BF1B00",
"id": 0,
@brainstorm
brainstorm / efika_card_build.sh
Created September 1, 2014 10:10
Buildbot scripts for Efika MX image/release engineering
#!/bin/bash
dcfldd if=/dev/$1 bs=1M count=1800 status=on statusinterval=1 | xz -z -T3 -c -e >$2
@brainstorm
brainstorm / kibana_pacemaker.json
Last active August 29, 2015 14:06
kibana_pacemaker.json
{
"title": "Pacemaker",
"services": {
"query": {
"list": {
"0": {
"query": "verb='GET'",
"alias": "GET",
"color": "#7EB26D",
"id": 0,
@brainstorm
brainstorm / Baton-dockerfile
Last active August 29, 2015 14:07
Baton Dockerfile
FROM ubuntu:12.04
ENV PGVERSION 9.3
ENV CK_DEFAULT_TIMEOUT 10
ENV IRODS_VAULT /usr/local/var/lib/irods/Vault
ENV TRAVIS_BUILD_DIR /tmp
RUN apt-cache search autotools
RUN apt-get update -qq
RUN apt-get install -qq odbc-postgresql unixodbc-dev build-essential libjansson-dev libjansson4 git wget autoconf
@brainstorm
brainstorm / Vagrantfile
Created June 24, 2015 07:58
BioStar ansible recipe
# -*- mode: ruby -*-
# vi: set ft=ruby :
# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
VAGRANTFILE_API_VERSION = "2"
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
# Every Vagrant virtual environment requires a box to build off of.
config.vm.box_url = "https://cloud-images.ubuntu.com/vagrant/trusty/current/trusty-server-cloudimg-amd64-vagrant-disk1.box"
config.vm.box = "base"
@brainstorm
brainstorm / JeOS
Created June 10, 2010 06:33
# https://help.ubuntu.com/10.04/serverguide/C/jeos-and-vmbuilder.html
sudo vmbuilder kvm ubuntu --hostname cloudbiolinux.local --suite lucid \
--flavour virtual --arch amd64 -o --libvirt qemu:///system \
--user ubuntu --pass password \
--addpkg unattended-upgrades --addpkg acpid --addpkg openssh-server
@brainstorm
brainstorm / Dockerfile
Created September 11, 2015 09:20
SeqControl Dockerfile
FROM phusion/baseimage
RUN apt-get update && apt-get install -y wget picard picard-tools samtools bedtools
RUN apt-get autoclean
RUN cd /tmp && wget http://labs.oicr.on.ca/files/6993/file/SeqControl_0.0.1.tar.gz
RUN cd /tmp && tar xvzf SeqControl_*.tar.gz && mv SeqControl_*/* /usr/local/bin
RUN rm -rf /tmp/SeqControl_*