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Articles tagged containers

  1. Things I'm Glad I Learned

    Skills, concepts, techniques, and models

    WARNING: This post was written with haste and therefore contains all kinds of typos, spelling errors, grammatical issues, and delusions of grandeur, wisdom, and writing ability.

    This post is intended as a living document—a gratitude journal of sorts—of some things that I'm glad I learned. I expect many of the items on this list will be relevant to computation biology, but that may change in the future.

    The big idea is that for every item on this list I am (A) glad that someone introduced me to it, and (B) think more people should know about it. This post is my chance to "pay it backwards", as it were; maybe someone else will be grateful for something they find for the first time on this list.

    It may also double as an inspiration list for future posts.

    My goal is to write a small blurb for each item …

  2. Take five minutes to simplify your life with Make

    WARNING: Because of the Markdown rendering of this blog, tab characters have been replaced with 4 spaces in code blocks. For this reason, the makefile code will not work when copied directly from the post. Instead, you must first replace all 4-space indents with a tab character.

    I use GNU Make to automate my data processing pipelines. I've written a tutorial 1 for novices on the basics of using Make for reproducible analysis and I think that everyone who writes more than one script, or runs more than one shell command to process their data can benefit from automating that process. I'm not alone.

    However, the investment required to learn Make and to convert an entire project can seem daunting to many time-strapped researchers. Even if you aren't living the dream—rebuilding a paper from raw data with a single invocation of make paper—I still think you can benefit …

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