These are the steps that I followed:
I read through the build instructions at:
In the section that says: "Windows MSYS2/MINGW64" I then realized I need a Compilation environment which is called MSYS, which contains a compiler: mingw64.exe
I then proceeded to download the file: msys2-x86_64-20241208.exe
from: the folder: https://repo.msys2.org/distrib/x86_64/
I started the installation on my Windows PC:
Then you RUN: MSYS2 MINGW64
This will open the build environment.
First thing to do is to check if the MSYS is up to date by typing: pacman -Syuu
And respond with Y
And respond with Y
Then you have to run it again after it has been upgraded: MSYS2 MINGW64
Also check that $MSYSTEM equals MINGW64 by typing: echo $MSYSTEM
Then update more components by typing the following one after the other and confirming by pressing enter.
pacman -S base-devel mingw-w64-x86_64-toolchain
pacman -S mingw-w64-x86_64-libdeflate mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2
pacman -S mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
pacman -S mingw-w64-x86_64-tools-git
Now download the C language source code base for SAMTOOLS from
These contain full source repositories which has the required libraries inside them:
Then I unzipped it. Probably a good idea to put it in a folder without spaces in the path, otherwise you will have to use "SAM\ TOOLS" with a backslash escape character to escape the spaces in the path.
Next step is to ensure that the folder where the compiler resides is in your WINDOWS Path variable:
(Depending on where you installed it initially)
E:\msys64\mingw64\bin
This is also where the SAMTOOLS will be put when it is compiled and installed.
Now you change to the folder where you have put the SAMTOOLS source code using the UNIX syntax in the console window of MINGW64
The following procedure is explained in : https://github.com/samtools/samtools/blob/develop/INSTALL
Then you have to change the current directory to where it was unzipped.
cd /F/Home/Development/SAMTOOLS/samtools-1.21
You can type LS to get the directory listing
You then run autoreconf to create the configure file if it does not exist
Next step is to type: ./configure
Next is to compile and link the exe:
just type: make
This will use the Makefile to build the EXE
At the end of this build process you will end up with the SAMTOOLS.EXE
You can now "install" this to the E:\msys64\mingw64\bin folder which is in your path by typing:
make install
This will result in the SAMTOOLS.exe being put in the folder together with all of its dependencies:
To test if it works you can open a normal windows command line window and change to the folder:
F:\Home\Development\SAMTOOLS\samtools-1.21\test\quickcheck
Then you simply check if it can open a BAM file :
samtools view 3.quickcheck.ok.bam
That is what is needed to compile SAMTOOLS.EXE
If you want to re-run the make for some reason, you will have to remove the config.mk file first otherwise it will not work. (rm = remove)
rm config.mk
rm /e/msys64/mingw64/bin/samtools.exe
./configure
and then proceed to run
make
and
make install
You can follow a similar procedure to build BCFTOOLS as obtained from:
https://www.htslib.org/download/
When you want to view a SAM file:
samtools view "F:\Home\Development\samtools-1.21\htslib-1.21\test\ce#1000.bam"
When you want to view a CRAM file:
samtools view "F:\Home\Development\samtools-1.21\htslib-1.21\test\ce#1000.cram"
samtools view "F:\Home\Development\samtools-1.21\htslib-1.21\test\ce#1000.cram"
When you want to create an index to allow you to search within ranges:
samtools index "F:\Home\Development\samtools-1.21\htslib-1.21\test\ce#1000.cram"
When you only want to view a specific range:
samtools view "F:\Home\Development\samtools-1.21\htslib-1.21\test\ce#1000.cram" CHROMOSOME_I:3-3
