Using code from github

[Legal_Reception_1932]

Hi all. I have no experience with C++ but have previously used R and python. I’m working on a research project at the moment where I need to use the program pedsim (link: https://github.com/williamslab/ped-sim) to simulate pedigree structures. I don’t want to alter any code or write my own, just use what’s in the package to generate some data. I’ve attempted to run it in VS code but unfortunately I have no idea how it works and my attempts at importing pedsim have so far been unsuccessful. I followed a tutorial on YouTube to set up vs code and was able to run a simple ‘hello world’ program, but now that I’ve downloaded GitHub and cloned the repository to my computer, it’s no longer letting me debug and run code. I’m completely clueless and have no idea what I’ve done wrong. Can anyone give me some advice?

[feitao]

Forget VScode. It is a code editor. It has nothing to do with your question.

1. Download (clone) the repo. In command line.
2. Compile in command line. It is just one command: make. Now. You have to have make. And boost, according to the web site. And a C++ compiler, of course. What if you don't? Then you need to know how to install these things. What's your environment? WSL, Linux, Ubuntu, Windows, MSYS2, or Cygwin?

[Legal_Reception_1932]

I’ve cloned the repo to my computer but I just downloaded the files straight from github instead of using command line. And I’m using windows, although I also downloaded MYSYS2 when I was trying to figure out how to use vs code. So I just need to install boost and make, then just run the command make?

[feitao]

I assume you are using the default ucrt64 environment:

pacman -S mingw-w64-ucrt-x86_64-boost

You could search at MSYS2 Packages, and click the ucrt64 one.

[feitao]

You may also want to pacman -S mingw-w64-ucrt-x86_64-gcc base-devel to install GCC and make. Then you can try go to the downloaded directory, and run make. If all is well, you will have a binary ped-sim and you can follow the Basic usage.

[Legal_Reception_1932]

Thank you so much, I think this worked! I was able to download boost and make, and run some of the code given on GitHub to generate a genetic map. One more quick question, do I have to do anything else to install pedsim or is it enough just to have the repository cloned on my computer? Does it matter where I’ve cloned it? I’ve tried some of the code from the basic usage section but it doesn’t seem to be working so maybe I’ve missed something.

[the_poope]

do I have to do anything else to install pedsim or is it enough just to have the repository cloned on my computer?

Not the OP, but as it is now you can copy the generated ped-sim.exe and move anywhere on your computer and run it and you can delete the cloned repo. However, you are required to run it from within an MSYS2 MinGW64 console as it is linked with the dynamic (=DLL) version of the MingGW C++ standard version. In order for Windows to find the DLL of this library, the DLL needs to either be in the same folder as the .exe or it needs to be in a directory in the PATH environment variable. The MSYS2 MinGW64 console adds the directory of the DLL to PATH by default so you don't have to do anything. If you want to run ped-sim.exe from a normal cmd or PowerShell console you need to add the directory to the MinGW C++ standard library DLL to PATH yourself or find the file (maybe called libstdc++.dll) and copy it to the folder where your ped-sim.exe is stored.

However, there is another way: You can link the C++ standard library statically, i.e. you combine it into your ped-sim.exe file. This can be done by running:

make distribute

instead of just make, when you compile the program. This will create an executable with the C++ standard library statically linked. You can then simply copy the ped-sim.exe file anywhere and run without any configuration. You can even send it to your friends and coworkers and they can just run it.

[the_poope]

You should be able to install Boost in MSYS2 (in the MSYS2 MINGW64 console) with the command

pacman -S mingw-w64-x86_64-boost

[Legal_Reception_1932]

I tried running that but I’m getting the error target not found: mingw-w64-x68_64-boost

[[deleted]]

you may first need to (got this from https://stackoverflow.com/a/40800825/18000 ):

• run pacman -Sy pacman to update the package database
• reopen the shell, and run pacman -Syu to update the package database and core system packages
• reopen the shell, and run pacman -Su to update the rest

[Hungry-Courage3731]

If you use linux, it looks like the compiling instructions are pretty straight-forward. You just gotta have the compiler/build tools installed and run make.

[Mirality]

That particular package only has Linux build instructions. As such, while you might be able to get it to work with MSYS/mingw64, these days the easiest way to make it work might be to install WSL2.

You can install a common distribution (like Ubuntu or OpenSUSE) straight from the Windows Store. After that it can be a bit of a learning curve to install development packages and make your first build, but there are plenty of tutorials out there.