May 2015 - Dave Tang's blog

Learning about Makefiles

programmingDavoMay 31, 20157

I started learning about Makefiles around the time I was learning about C roughly a year ago. I still don't know much about Makefiles or C, but I'm revisiting Makefiles because I'm interested in using them for purposes of reproducible research. Initially I thought Makefiles were simply text files that were mainly used to help...

Getting started with Bpipe

bioinformaticsDavoMay 28, 20153

I have been using simple shell scripts for creating my bioinformatic pipelines. I define variables that can be used as parameter settings throughout the script, use some basic Unix tools for creating my output file names, and simply check the existence of files to see whether a step has been run or not. You can...