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Kale
06-22-2018, 06:23 PM
This is probably a stupid question, but where are the executables for qpgraph and qpreroot? Are there executables? If not how do I run them? I know how to set up the graph files and (pretty sure) the parfile, the commands are on the admixtools github - Just need to find the darn 'do stuff' file to reference in the terminal!

MacUalraig
06-22-2018, 08:00 PM
This is probably a stupid question, but where are the executables for qpgraph and qpreroot? Are there executables? If not how do I run them? I know how to set up the graph files and (pretty sure) the parfile, the commands are on the admixtools github - Just need to find the darn 'do stuff' file to reference in the terminal!

EDIT: Whatever anyone else is this situation would do, DO NOT run 'make' anything, it deleted everything in my bin directory >:(
...maybe someone can help me with this too. After my bin directory was deleted (it only had qpdstat executable with parfile, some logfiles, and a file with the commands),
I put everything back as it was. Now it won't work.
I ran a simple stat...
MbutiDG Ust_Ishim MA1 AG3
The logfile told me there are 3 samples under the MbutiDG label and that was all the run did.:confused:

That's all very well but the makefile does make the two exes you asked about (as long as you have gsl installed)

https://github.com/DReichLab/AdmixTools/blob/master/src/Makefile

qpGraph: $(NLIB) qpGraph.o gslqp.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o

qpreroot: qpreroot.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o

Running make is pretty de rigeur on unix... :-)

Kale
06-23-2018, 03:05 AM
I'm not exactly sure what 'make' entails, but is it possible to just copy the executables from somewhere else? I don't want anything else to break! Please for the love of god let them be copyable.
I installed gsl (2.1) and openblas (2.2)
...here's the errors I get before terminal poops itself

/usr/bin/ld: cannot find -lgsl
/usr/bin/ld: cannot find -lopenblas
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'qp3pop' failed
make: *** [qp3pop] Error 1

Do I have the wrong versions of gsl + openblas or something? Those are the ones that wanted to install with 'dnf install ___'

EDIT: I figured out what went wrong with qpdstat, there is a line in the parfile, "poplistname" that has to be changed to "popfilename". Ugh, the former (default) is inherently inferior to the latter, why redundicize?

...New philosophy, doctors, physicists, etc. are just those that couldn't cut it trying to diagnose Linux problems.