I recommend doing this sort of process for any programming thing you use that might interfere with the system version. I think 'pip' and 'python' also get re-aliased to whatever is in /path/to/personal/python/bin/., so it's like you never even notice the difference. bash_profile to do this automatically for every terminal. For that terminal session (and other sessions after running source again), anything you install via /path/to/personal/python/bin/pip will not interfere with the OSX system python. To use your personal python run source /path/to/personal/python/bin/activate.Do the same as the above but with a different dir and run virtualenv -p /path/to/pypy/download /path/to/personal/pypy. now would be a good time to also get pypy - python thats 3-4x faster than CPython.sudo apt-get install python-dev # Just found out that this is an unmentioned dep.There's many ways to do this but i'll go through doing it for Python: This is good if you want to use IGV/R from a remote machine with x-forwarding over ssh.įor programming languages/intepreters, it's always best NOT to use the system version and instead reinstall them in a virtual environment. With those out of the way, I would next get xquartz, which is X11 for OSX. Installing/Uninstalling is waaay easier in Homebrew, as is updating. Fortunately, unlike Macports, Homebrew doesn't require you to be root to install, (or install most things via it), so use of Homebrew is always recommended over Macports. Installing Homebrew however is a piece of cake, provided your cool with executing whatever a webserver happens to reply with. Source should be the last option, as you can easily half-install Macports, and that will lead to a huge headache down the road. If that doesn't work, reboot, sleep on it, and try installing it again later, rather than from source. Far better to install the precompiled package. Macports, in my experience, is a pain to install from source. With that done, you should really get Macports and then Homebrew. You can do this from the terminal by running "sudo xcodebuild -license" Once both are installed you need to agree to the XCode licencing agreements, stipulating that Apple may call upon you to sacrifice your first born son as a test of your faith. This should really be the absolute first thing anyone does, since many things get linked to XCode's libs, so installing XCode later may mean reinstalling things later. You don't need to be part of the Apple Developer Program (which is $99 a year), but rumor has it that's about to change as Swift2 becomes more mature. To compile anything worthwhile, you need XCode and Command Line Developer tools, but before you can get that you'll need a Developer Account. Looking forward (well, not really) to see if this will break at the next system upgrade.Įveryone uses their computer differently (vim vs emacs!) and its no different on OSX, so this is really just my opinion: We ended up installing Xcode then homebrew (+ coreutils, wget.) and Anaconda for Python. Marking Chris Miller's answer as correct, although I used pieces of many answers, including some from Twitter. That plus the fact that I have personally little experience being in the driving seats of Macs. It seems that over the years package managers for Macs have gone in and out of fashion rapidly, thus I do not know which way to go. Something else that is trendy (and VERY stable) right now?.What is the first thing or two you would do to make a Mac Book ready for bioinfo software installation? I know lots of you top bioinfo users on Biostars are using macs, so here is the question: I need to help her set up her mac book so that she can use it in a bioinfo role for 'light analyses', although the laptop is pretty powerful. She's having trouble updating gcc and installing things like wget and vcftools. One of our students just got a brand new mac book running El Capitan.
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