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I am very new using Linux. I need to use some programs (plink; https://www.cog-genomics.org/plink/ and ldsc: https://github.com/bulik/ldsc) that are usually ran in Linux. I am a windows user and I have installed Cygwin to emulate Linux. However, I cannot make them work. I have downloaded all files and unzip them in the main directory but they do not work. The command line does not recognize the commands.

Any ideas about how to run these programs using Cygwin?

Thank you so much in advance. With all good wishes.

JuanJMV
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  • Any reason you're using Cygwin instead of WSL? – Martheen Jul 17 '22 at 15:11
  • Thank you so much @Martheen. I have tried with WLS but using LDSC the analyses take so long, something that should be done in seconds takes hours. Any ideas to fix this? – JuanJMV Jul 18 '22 at 09:01
  • Might be slower IO on WSL, either try setting up a VM or dual boot (maybe just a live USB session is enough if you can't spare the partition). – Martheen Jul 18 '22 at 09:22
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    Cygwin, as useful as it may be, does not emulate Linux. If you have the source code to the programs you need, you can try to recompile them for Cygwin. – user1934428 Jul 21 '22 at 09:35

1 Answers1

2

Solution #1 (easy)
use the Windows version at https://www.cog-genomics.org/plink/

Solution #2 (more difficult) as clearly the code is lacking of any Autoconf/Cmake configuration set up.

Build requires the packages: make, gcc-g++, liblapack-devel, cygwin-devel, zlib-devel

Download the source code in tar.gz format from
https://github.com/chrchang/plink-ng/releases?page=1

and then

tar -xf plink-ng-2.00a3.3.tar.gz
cd plink-ng-2.00a3.3
ln -s /usr/include zlib-1.2.11
cd 1.9
make ZLIB="-lz" BLASFLAGS="-llapack -lblas"
matzeri
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