Program and Scripts

Ideally, you could refer the whole world --- or at least, the significant portion thereof that want your code --- to your (public mirror) Git repository. But unfortunately, the whole world does not (yet) use Git ("I know it was you Fredo, I know it was you, and it breaks my heart."). Sad. Sooooo sad. But true. So the only recourse is for you to send these tortured souls an archived snapshot of your code via e-mail. I'll pause now to let you finish retching/sobbing/lamenting/venting. ... Back? Anyway, Git has a neat "archive" command that helps you create the required archive, but perhaps it does not have the most friendliest interface in the world. Drop the following script anywhere on your path name it "git-targz" and set its executable bit on. Then invoking "git targz TARBALL-FILEPATH" will create a tar'd and gzip'd bundle of your (repository's) current HEAD. Similar scripts for bzip'ing and plain old zipping can easily be created by varying the final command, and are shown after the tar + gzip script.

Here I present a script that provides diagnostics about the current Python execution context, or the Python environment of the interpreter passed as an argument. As a Python developer, I have multiple Python versions side-by-side for testing purposes, using scripts that munge my $PATH variable to "import" and "unimport" different versions of Python as I need them. While "which python" is always available, many times I want to know things like, "what is the version of the current default Python?" or "where is the current Python's 'site-packages' directory?". Though all this information is usually one or two commands away, it can be pretty tedious jump through these hoops every time this information is required. Also, often mature systems that have gone through various systems administrators and upgrades have both legacy and current stuff scattered all over the place, and it can be a hassle trying to figure out where the site packages and other components of a particular installation of Python are located.

htop is an interactive process viewer, like top, but greatly enhanced in many respects. The main code base relies on the virtual directory '/proc', which does not exist in OS X. However, thanks to the generosity and smarts of Andy Armstrong, an OS X port is available, and can be cloned by:

This OS X Dashboard Widget displays a "cheat sheet" style summary of selection of Emacs commands:

You can download it from here:

This OS X Dashboard Widget displays a "cheat sheet" style summary of selection of Git commands that are commonly used in most development workflows:

You can download it from here:

The following script takes a space separated list of GenBank numbers as input, and then uses BioPython to download the corresponding sequences from GenBank, strips off all non-coding nucleotides, gives the sequences sensible names, and assembles them into a FASTA file.

msBayes is a suite of tools that support a Approximate Bayesian Computation approach for phylogeographic analysis, estimation and hypothesis testing.