Niknafs

#!/bin/bash

# Script for installing tmux on systems where you don't have root access.
# tmux will be installed in $HOME/local/bin.
# It's assumed that wget and a C/C++ compiler are installed.

# exit on error
set -e

TMUX_VERSION=1.8

Niknafs

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

Niknafs

Background

Last week when trying to generate some awsome summary graphic, I came across the painful ordeal of trying to combine ggplot elements with a number of regular R graphic elements.

First things first, I had used grid.arrange module from gridExtra package to juxtapose ggplot elements in a panel figure. Furthermore, I had combined regular R [read non-ggplot] figures thru the good old par functionality.

Brief summary:

We will be making calls to viewport module from the gridBase package to generate---guess what---view ports into which ggplot objects are plotted. Interestingly, ggplot elements need not be a single simple ggplot object, but could be an arrangement of multiple objects bundled together using arrangeGrob module from gridExtra.

Niknafs

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

Niknafs

# if get recieve.denyCurrentBranch error try to pull from
# the repository instead of pushing. Alternatively just
# switch to a tmp branch.

# Permanently going back to previous commit
git reset --hard 123abc

# Checkout a previous commit into a separate branch
# without a branch name it will be in a headless state
git checkout -b old-state 123abc

Niknafs

This document will cover the steps involved in installation of `python-igraph` package for python 2.7. For python 3.x, the steps will likely be similar, but possibly not identical.

The python-igraph package requires `cairo` library, and `py2cairo` python package. `cairo` is a 

Niknafs

Overview

This document will cover the steps involved in installation of python-igraph package for python 2.7. For python 3.x, the steps will likely be similar, but possibly not identical.

The python-igraph package requires cairo library, and Pycairo python package, and igraph C core. cairo is a 2D graphics library with support for multiple output devices and Pycairo is a set of python bindings for cairo graphics library.

In this document, it is assumed that the user does not have root access and thus uses --prefix to indicate a local directory where /lib and /bin can be located, for which the user has write privilage.

Cairo

Niknafs

BAM files generated by Exome sequencing at several sequencing service centers do not comply with the required specs assumed by the GATK tools. Here are steps involved in processing these raw bam files to prepare them for analysis by other tools.

These steps are formatted as a sequence of bocks in a make file. Before getting started, make sure that you have specified the path to the following pre-requisites in the header of the make file.

Prerequisites:

# general workspace path definitions
SRC=/my/source/directory/with/installed/tools/
temp_folder=/mnt/hn07_disk001/my-project/tmp/
SCRATCH=/mnt/hn07_disk001/my-project/pipeline 

Niknafs

1. Install the required linux library

apt-get install libxmu-dev

2. Install matlab component runtime

From the directory ([MCR dir]) with instal script run:

Niknafs

Problem:

Often, after restarting my machine (OS X Yosemite, version 10.10.5) I encounter the following error the first time I run docker quick start terminal. The problem is discussed in great length here, but none of the proposed solutions seemed to fix it on my machine.

Specs

OS X Yosemite version 10.10.5
Docker version  1.9.1