Setup for VirtualBox VM running Ubuntu 14.04 on OS X Mavericks

Fri 06 February 2015 — Filed under notes; tags: linux, mac, virtualbox read more

Here are my notes for setting up an Ubuntu VM to work on some web applications. This is intended to be a sandbox for development, so I'll err on the side of convenience (at …

Compiling bcl2fastq v2.15 on Ubuntu 12.04 and 14.04

Wed 27 August 2014 — Filed under notes; tags: linux read more

Illumina provides a program for demultiplexing sequencing output called bcl2fastq. They get a gold star for releasing the source - the downside is that they release binaries only for RHEL/CentOS, and no build instructions for Ubuntu. So …

Creating lists containing variables

Thu 12 June 2014 — Filed under notes; tags: elisp read more

I learned a bit about list creation in elisp today. Here's how you join a list of strings in elisp:

(mapconcat #'identity '("" "path" "to" "someplace") "/")

But I learned (thanks to legoscia on stackoverflow) that simply replacing an element in the list with a variable results in an error:

(let ((path …

sqlite dict factory

Tue 10 June 2014 — Filed under notes; tags: python, sqlite read more

Probably not as efficient as using the sqlite3.Row class, but works when actual dict objects are required. Adapted from https://docs.python.org/2/library/sqlite3.html.

import sqlite3

def dict_factory(cursor, row):
    return {col[0]: row[idx] for idx, col in enumerate(cursor.description)}

con = sqlite3.connect(":memory …

Setting up a new mac

Sun 20 October 2013 — Filed under notes; tags: mac read more

Installing R packages

Mon 22 March 2010 — Filed under notes; tags: R-language read more

Notes to myself about installing R packages.

Installing from CRAN

install.packages(c("ape","sqldf","ROCR"), repos="http://cran.fhcrc.org/", dependencies=TRUE, clean=TRUE)

Bioconductor

source("http://bioconductor.org/biocLite.R")
biocLite(c("Biostrings","BSgenome …