ADMIXTOOLS version 5.0 6/28/18 (for Linux and Mac)
Best is to recompile on your system.
You will need to be able to link GNU Scientific library(gsl) , BLAS, gfortran, and prpbably lapack.
This Makefile expects opeenblas but other versions of BLAS should be OK. Edit the Makefile
appropriately.
cd src; make clobber; make all; make install. Eexcutables will be in ../bin
A Makefile that worked for a Mac (El Capitan) is in src/Makefile.mac
Nick Patterson ADMIXTOOLS version 5.0 6/28/18 (for Linux, Mac, and Windows)
For Linux and Mac:
Best is to recompile on your system.
You will need to be able to link GNU Scientific library(gsl) , BLAS, gfortran, and prpbably lapack. This Makefile expects opeenblas but other versions of BLAS should be OK. Edit the Makefile appropriately.
cd src; make clobber; make all; make install. Eexcutables will be in ../bin
A Makefile that worked for a Mac (El Capitan) is in src/Makefile.mac
Nick Patterson
For Windows
You can download the executables from the "Releases" section. Should work on x64 Windows 11 (maybe 10 too).
Compiling it yourself - Build tools
If you want to compile it yourself, you'll need for Windows all the packages mentioned for Mac and Linux, and more. But before you start, you'll need these individual components from Visual Studio Build Tools (2022):
- Windows Universal C Runtime
- Windows 11 SDK
- MSVC v143 - VS 2022 C++ x64/x86 build tools
For the SDK, I'm using version 10.0.22621.0, and for the build tools, v14.38-17.8.
To download and install these, I recommend using the Visual Studio Installer (the thing that gets installed before Visual Studio itself, and helps you manage its versions). Once the installer is running, navigate to the "Available" tab, and click "Install" on "Visual Studio Community 2022".
On the next menu, go to the "Individual Components" tab, and select the three options you see selected on the right in the SS below (the same three are selected on the left too, but the list is huge so the third one isn't on screen):
Click install.
Once done, look around in your filesystem for the cl, lib, link and nmake tools. They should've been installed too now, and will be in the same folder. On my machine, the folder looked something like this:
C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.38.33130\bin\Hostx64\x64
Once you find the folder on your machine, add it to PATH.
Downloading the dependencies
We can now start gathering the dependencies for AdmixTools on Windows. We'll need all the ones mentioned for Mac and Linux, and then some. Here's where I got them, with the versions I used in parantheses where relevant:
I put these all in a folder called CppLibs. GSL and OpenBLAS should be ready to go already. sys and some parts of libunistd need to be compiled.
For the sys repo, make a folder called sys under your CppLibs folder, and then clone the repo I linked to for this dependency under that folder. Your directory structure should like this:
CppLibs/
sys/
sys/
.git
times.c
times.h
LICENSE
For the other three dependencies, you can download/clone them directly into CppLibs, don't need to go one-level deeper like we did here. For example:
CppLibs/
libunistd/
.git
unistd/
unistd.cpp
getopt.cpp
sigaction.cpp
Building the dependencies
Once you've downloaded everything, another set of folders you want to dig for, are the ones being added to the CFLAGS macro in src/Makefile.windows. The same ones also used in src/nicksrc/Makefile.windows fwiw. We'll start to need them now. I'll refer to the paths for these folders (aka "include paths") on your PC as <path_to_ucrt_h>, <path_to_um_h> etc.
Build sys/times
Refer to the directory tree for the sys dependency shown before. Navigate via PowerShell to the directory for sys, and then to the subdirectory that contains the times.c and times.h files. Then, do:
cl /I <path_to_ucrt_h> /I <path_to_um_h> ... /c .\times.c // I ended up needing the include paths from lines 5, 7, 8, and 12 of Makefile.windows
lib .\times.obj
This should have created a times.lib file in the same directory. We'll need it later.
Build getopt, unistd, and sigaction
Now, refer to the directory tree for the libunistd dependency shown before. We need to build three libs in there, and they'll all be in the unistd subdirectory.
For better management, to start, create a folder called libs under unistd, so that the directory tree looks like this:
CppLibs/
libunistd/
.git
unistd/
unistd.cpp
getopt.cpp
sigaction.cpp
libs/
For the next part, you need the paths to Uuid.lib, libcmt.lib, and oldnames.lib
Now do:
cl /I <path_to_ucrt_h> /I <path_to_um_h> ... /c .\unistd.cpp // I ended up using all the include paths
lib .\unistd.obj /out:libs\unistd.lib
cl /I <path_to_ucrt_h> /I <path_to_um_h> ... /c .\getopt.cpp
lib .\getopt.obj /out:libs\getopt.lib
cl /I <path_to_ucrt_h> /I <path_to_um_h> ... /c .\sigaction.cpp
lib /LIBPATH <path_to_uuid.lib> /LIBPATH <path_to_libcmt.lib> /LIBPATH <path_to_oldnames.lib> .\sigaction.obj
mv .\sigaction.lib .\libs\
Now, look at the contents of the libs folder you created. It should have three static libraries in it, the sames ones we just made.
Build AdmixTools
Now, navigate to the AdmixTools/src, and then do:
nmake /F Makefile.windows clobber
nmake /F Makefile.windows all
nmake /F Makefile.windows install
nmake /F Makefile.windows clean
Look inside the AdmixTools/bin folder, and you should have your executables there!
PS \AdmixTools\bin> .\qpfstats.exe
no parameters
## qpfstats version: 540
Now add this folder to PATH, and you're done!
-Tushar