GDB in threaded code

GDB (https://www.gnu.org/software/gdb/ ) is a handy way to debug command line applications. But in the case of applications that are running many threads, it doesn't by default follow a single thread, so as you step through the code it jumps between threads and it's easy to lose track of where you are. The solution is the scheduler-locking command, which forces the stepper to only step through one active thread at a time.

(gdb) set scheduler-locking on

See here for details: https://sourceware.org/gdb/current/onlinedocs/gdb/All_002dStop-Mode.html

Creating a Hyperbook in Microsoft Word

When someone creates a document they'll possibly set up a table of contents which conveniently links to the chapter headings they've created. They'll very likely provide hyperlinks to their sources or references so it's easy to go out on the web and find the sources. But it's pretty rare to provide handy links inside the document pointing to other places in the document - a hyperbook. Now, there's no reason not to keep providing outside links as well, but a good hyperbook is like a self-contained Wikipedia - lots of good information and lots of links to related subjects of interest directly on the page.

To insert internal links into a document in Microsoft Word, do the following.  On the Insert tab, there's a Links panel. Click that, then Link, then Insert Link. The dialog that comes up offers a variety of ways to insert internal links. Very nice for creating hyperbooks.

Force-closing an SSH connection

On occasion when I'm using SSH to connect to a remote server, I run an application that hangs. If the terminal's running inside a GUI, you can always close down the entire terminal and restart it, but there's an easier way: hit Enter, then type "~." (squiggle dot) That force-closes the SSH session leaving your terminal intact. I learned this from SuperUser:

https://superuser.com/q/467398

Downloading files from Google Cloud

In doing some testing with GATK 4, I found myself in need of downloading files from Google Cloud. Google Cloud likes to use URL's
that start with gs: For example, the URL for some tumor data is

gs://gatk-best-practices/somatic-b37/HCC1143.bam .

You can't just visit that URL in your browser though; or at least I couldn't. I had to install gsutil as described here: https://cloud.google.com/storage/docs/gsutil_install#linux . This is one of those weird installs where they provide a script online that you can run; a bit dangerous, but at least they don't ask for sudo. It downloads about a gazillion files then asks permission to muck with your settings. I said no, of course, and it gave me a couple of files to source if I wanted. One of them had to do with providing autocomplete, but the other one simply added a directory to the path, so I created
an environment module to do that work. Now I can download the files I need:

$ gsutil cp gs://gatk-best-practices/somatic-b37/HCC1143.bam .

Github offers successor options

Github is putting some thought into what happens to to your repositories if you're "unable" to manage them - a kind way of saying if you die. Nothing I have would have any consequence, but certainly I'm involved with some organizations that would need taking over. Here's how you name a successor for your repositories:

https://github.blog/changelog/2020-05-11-account-successors/