jfear

channels:
  - jfear
dependencies:
  - sratoolkit==2.8.1

jfear

# -*- mode: ruby -*-
# vi: set ft=ruby :
# for issue at https://github.com/PacificBiosciences/Bioinformatics-Training/issues/15
VAGRANTFILE_API_VERSION = "2"

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
  config.vm.box = "ubuntu/xenial64"
  config.vm.network "forwarded_port", guest:8080, host:8080
config.vm.synced_folder "/Volumes/Promise_Pegasus/fearjm/pacbio_prelim", "/home/ubuntu/pacbio_prelim", :mount_options => ["dmode=755", "fmode=644"]  config.vm.provider "virtualbox" do |vb|
    vb.customize ["modifyvm", :id, "--memory", "20048"]

jfear

sudo yum install libmpc-devel mpfr-devel gmp-devel

cd ~/Downloads
curl ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-4.9.2/gcc-4.9.2.tar.bz2 -O
tar xvfj gcc-4.9.2.tar.bz2

cd gcc-4.9.2
./configure --disable-multilib --enable-languages=c,c++
make -j 4
make install

jfear

This is a set of useful links

Professional

• Individual Development Plan: https://myidp.sciencecareers.org/

Programing

Git

• Interactive introduction to GIT: https://www.codecademy.com/learn/learn-git
• Gits manual: http://gitref.org/index.html

jfear

# Copied from:
# https://raw.githubusercontent.com/thisisarray/GitHub-Issues-Process/master/set-github-labels.sh

echo ''
echo 'This script will remove the GitHub default labels and create the 80|20 process labels for your repo. A personal access token is required to access private repos.'

echo ''
echo -n 'GitHub Personal Access Token: '
read -s TOKEN

jfear

# Tmux
function tmux() {
  # Make sure even pre-existing tmux sessions use the latest SSH_AUTH_SOCK.
  # (Inspired by: https://gist.github.com/lann/6771001)
  local SOCK_SYMLINK=~/.ssh/ssh_auth_sock
  if [ -r "$SSH_AUTH_SOCK" -a ! -L "$SSH_AUTH_SOCK" ]; then
    ln -sf "$SSH_AUTH_SOCK" $SOCK_SYMLINK
  fi

  # If provided with args, pass them through.

jfear

#!/bin/sh

set -e

SESSION_NAME=$(basename "$(pwd)")

if tmux has-session -t $SESSION_NAME 2> /dev/null; then
  tmux attach -t $SESSION_NAME
fi

jfear

"""Plot heatmap of all genes.

Plots the tpm normalized zscores of all genes as a heatmap.
"""
import numpy as np
import pandas as pd
from scipy.stats import fisher_exact
import matplotlib as mpl
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
import matplotlib.pyplot as plt

jfear

README

Create a template service file at /etc/systemd/system/secure-tunnel@.service. The template parameter will correspond to the name of target host:

[Unit]
Description=Setup a secure tunnel to %I
After=network.target

jfear

#!/bin/bash
conda create -n jupyter jupyterlab jupytext nodejs nb_conda ipywidgets nbdime ipympl jupyterlab-git
source activate jupyter
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install jupyterlab_vim
jupyter labextension install @jupyterlab/git
jupyter serverextension enable --py jupyterlab_git
jupyter labextension install @jupyterlab/toc
jupyter labextension install jupyterlab_bokeh
jupyter labextension install @ijmbarr/jupyterlab_spellchecker