After installing Anaconda python in hopes to learn some python via iPython notebooks, I found that the most basic commands (like starting the navigator / new notebook / etc) did not work from the Terminal. I was getting all sorts of confused about what was going on. The problem was simple: 

Anaconda's installation does set all the paths properly, but the problem is using fish as the default shell. Because I'm not using bash as the default shell, I don't get access to any of the PATHs that are set by ~/.bash_profile! 

One option would be to try manually setting all those environment variables in fish.config (or whatever it's called) but that seems like a pain.

Another option, from here, it to try this: "Keep your default shell as Bash and simply add the line exec fish to the appropriate Bash#Configuration files,"

I did that - adding exec fish to the end of ~/.bash_profile, and changed back to bash as the default shell. Now, when opening a new terminal window, fish opens and running which python finally gives me /Users/garylarson/anaconda/bin/python. 

From http://stackoverflow.com/questions/28761323/how-to-include-external-library-boost-into-clion-c-project-with-cmake
Essentially I modified the default CMakeLists.txt file to be:

How to actually see the location of a symbolic link, e.g. the command "which java" returns /usr/bin/java or whatever.

Use this instead:
readlink -f $(which java)

Note: The below was turned into a script called "listalljobs" on my search path. So I just run "listalljobs" and it shows what I want. The "Name=mpi" part is because all my scripts submitted to run on the cluster contain that string. So for non-Wang-Schmidler stuff, I'll need to modify the command below.

How to quickly learn what directories my jobs belong to when I'm running lots of jobs. (this removes need for my "runIDinformation.txt" file! Yay.)

• run the below command
• paste its output into Sublime Text
• use Ctrl + Command + G to select all unwanted text and quickly remove unwanted lines
• continue with Sublime text until you have something like

8146477 pfConcept4-25prots
8146478 pfConcept4-25prots
8146479 pfConcept4-25prots
...

scontrol show job | grep --color -E "UserId=gjl7|WorkDir=/hpchome/sysbio/gjl7|Name=mpi"

Finally, an explanation! File is attached right here.

I had some kind of problem ... don't even remember what it was. But I found a fix that worked... cleaning up my Desktop... here's the fix.

my fix for linux dropbox

on jan 1, 2015, I did:

cp ~/.dropbox-dist/dropbox-lnx.x86_64-3.0.3/libxml2.so.2 ~/.dropbox-dist/dropbox-lnx.x86_64-3.0.3/libxml2.so.2_BACKUP20150105

killall dropbox

rm ~/.dropbox-dist/dropbox-lnx.x86*/libxml2.so.2

dropbox start

From: http://apple.stackexchange.com/questions/66422/change-all-the-txt-files-to-md-files-in-a-certain-folder

e.g. to replace a bunch of files in a folder which end in .pdb, and change the extension to .txt, run:

find . -iname "*.pdb" -exec bash -c 'mv "$0" "${0%\.pdb}.txt"' {} \;


Note: The website above says it does this "recursively" by which they may mean it acts on subfolders, too. I haven't tested this, so be careful!

• Open a terminal console
  
• Enter the command uname -m (uname prints system information; -m option prints the machine hardware name.)

If you have a 32-bit system, uname -m will return a value of i686. A 64-bit system will return a value of x86_64.

This will give a similar setup like Fugu on Mac. Just be careful when looking at a browser window whether you are looking at the local folder or the remote SSH folder!