elipapa

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elipapa

Set up a new os x laptop

Steps to setup a new OS X laptop with a data science & computational biology development environment.

Last updated: 7 Jan 2017 macOS: Yosemite => Sierra

Sure you could try to do this from dotfiles, but historically something has broken and required manual input anyway. So, inspired by the pragmatism of paul irish bash setup script and a few other gists written in markdown like this, I rolled my own.

Some design considerations:

elipapa

The minimal set of steps to get a decent command line on a server

using homebrew, apt-get or whatever you have access to:

• install git
• install zsh

Directly from prezto install instructions

elipapa

#!/usr/bin/env python3

## converting journey android app entries to dayone entries using the the dayone-cli limited input options

# first download all single posts zip files and place them in the folder of the script. Then run
# unzip '*.zip'
# where quotes are important!
#
# Then run this script in the folder

elipapa

#!/bin/bash
while true; do
  until [[ $usedspace -ge 60 ]]; do
    for file_ready in queue/*.downloaded; do
      filepath=${file_ready%.downloaded}
      file=${filepath##*/}
      srsid=${file/.*/}
      if [ ! -e "queue/$srsid.decompressed" ]
      then
        echo "Decompressing $srsid ..."

elipapa

#!/usr/bin/env bash

# Installation with this script in your $PATH:
#   $ git config --global alias.deploy '!git-deploy'

# When in the repo just go:
#   $ git deploy ssh://user@server/a/path/to/repo

# which creates a bare repository bare.git in that remote directory
# and copies the working tree in the directory

elipapa

#!/usr/bin/env bash

# USAGE:
# 0. install jq from https://stedolan.github.io/jq/ if not already present
# 1. make this script executable
#     chmod u+x gene2ensembl.sh
# 2. then run it on a gene list with one gene ID per line
      ./gene2ensembl.sh genesymbollist.txt > ensembl_list.txt

# NOTE: this command does not run in parallel on purpose

elipapa

Kubernetes clusters using preemtible instances

Motivation

People experimenting with kubernetes clusters on the GKE not necessarily have money to keep a full cluster on at all time. GKE clusters can be easily resized, but this still incurs in the full instance cost when the cluster is up.

Google has added preemptible instances that are ideal for many

elipapa

# Inspirations:
# http://mutelight.org/practical-tmux
# http://zanshin.net/2013/09/05/my-tmux-configuration/
# http://files.floriancrouzat.net/dotfiles/.tmux.conf
# http://stackoverflow.com/questions/9628435/tmux-status-bar-configuration
# https://github.com/Lokaltog/powerline
# https://github.com/remiprev/teamocil
# http://superuser.com/questions/74492/whats-the-best-prefix-escape-sequence-for-screen-or-tmux
# http://blog.hawkhost.com/2010/07/02/tmux-%E2%80%93-the-terminal-multiplexer-part-2/
#

elipapa

#!/usr/bin/env bash
# assuming your ES is at http://localhost:9200


# set all existing indices to 0 replicas
curl -XPUT "http://localhost:9200/_settings" --data '{"index":{"number_of_replicas": 0}}'

# set marvel index to default 0 replicas
curl -XPUT "http://localhost:9200/_template/custom_marvel" --data '{
        "template": ".marvel*",