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Thread: How to run Admixtools

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    How to run Admixtools

    I was wondering if someone could give a step by step guide on how to run Admixtools?

    I've downloaded Admixtools from github and have Linux Mint (18.2 cinnamon) installed on a USB and can boot from that, but have no idea on what to do next. Do I need to download anything else apart from Admixtools?

    Any help would be much appreciated!
    Last edited by Bas; 09-30-2017 at 11:46 PM.

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    Quote Originally Posted by Bas View Post
    I was wondering if someone could give a step by step guide on how to run Admixtools?

    I've downloaded Admixtools from github and have Linux Mint (18.2 cinnamon) installed on a USB and can boot from that, but have no idea on what to do next. Do I need to download anything else apart from Admixtools?

    Any help would be much appreciated!
    Which executable program inside admixtools do you want to run? In any case you need a parameters file ( models are the texte files which name begins with "par" in one of the subfolders of admixtools, don't recall which one; for example "parqpAdm"). You have to adapt the parameters file to the genetic datas you want to use ( always in EIGENSTRAT format) , and place it in the "bin"-folder. You have of course to rewrite the files needed by the program you want to run ( for example "left" and "right" for qpAdm) Once you have done that, it's very simple. You open a terminal, go to the "bin" folder ( for me: cd genetic/asmixtools5/bin), and write a command line ( for example for qpAdm) :" ./qpAdm -p parqpAdm".
    Using admixtools is elementary. The difficult thing is what happens before: converting, pruning, merging, etc. For all that you'll need to dowload programs like Plink, vcftools, eigensoft ( and perhaps others, depending on what you want to do).
    note: I have no real experience of using linux from a usb. I have myself installed my linux ( now fedora25) on a virtual machine.
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     Bas (10-02-2017)

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    Thankyou for your reply anglesqueville. I wanted to run D-stats and as I said, had Linux Mint on USB.

    I booted Mint and copied Admixtools from another USB and pasted that on the Mint desktop. So far, so good. Then I opened a terminal in the src folder and typed:

    make clobber
    make all

    After 'make clobber' it looked ok. And if I remember correctly, the next step after 'make all' this would have been 'make install'. Unfortunately,at the 'make all' command, I got a string of error messages, (coming from the /nicksrc folder I think) each with a different number (bolded below to highlight) saying:

    'home/mint/Desktop/AdmixTools-1.0.1/src/nicksrc/gds.c:672: undefined....'

    and after this, right at the end of the output:

    collect2: error: ld returned 1 exit status
    Makefile:76: recipe for target 'qp3Pop' failed
    make: *** [qp3Pop] Error 1
    [email protected] -/Desktop/AdmixTools-1.0.1/src $


    I feel I am quite close but have no idea to overcome this problem.

    Here's an image of the screen-sorry for the potato quality...

    IMG_20171001_191639.jpg
    Last edited by Bas; 10-02-2017 at 04:27 PM.

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    I don't want to be pessimistic, but I was quite unable to install admixtools on ubuntu, mint, even scientific linux. I had problems with the version of the compilater. That said, make sure you have the following biblios ( openblas and lapack):

    openblas-threads64_-0.2.19-4.el7.x86_64
    openblas-serial64_-0.2.19-4.el7.x86_64
    openblas-openmp64-0.2.19-4.el7.x86_64
    openblas-openmp-0.2.19-4.el7.x86_64
    openblas-threads-0.2.19-4.el7.x86_64
    openblas-threads64-0.2.19-4.el7.x86_64
    openblas-0.2.19-4.el7.x86_64
    openblas-openmp64_-0.2.19-4.el7.x86_64
    openblas-serial64-0.2.19-4.el7.x86_64
    openblas-devel-0.2.19-4.el7.x86_64
    openblas-static-0.2.19-4.el7.x86_64
    openblas-Rblas-0.2.19-4.el7.x86_64
    blas-devel-3.4.2-5.el7.x86_64
    lapack-devel-3.4.2-5.el7.x86_64
    lapack64-3.4.2-5.el7.x86_64
    blas64-3.4.2-5.el7.x86_64
    blas64-devel-3.4.2-5.el7.x86_64
    lapack64-devel-3.4.2-5.el7.x86_64
    lapack64-static-3.4.2-5.el7.x86_64
    lapack-static-3.4.2-5.el7.x86_64
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     Bas (10-02-2017)

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    If you want to pm me the full output not just the bit you screenshot I might be able to give you some 'pointers' (C joke sorry).
    Last edited by MacUalraig; 10-02-2017 at 07:20 PM.
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    Quote Originally Posted by MacUalraig View Post
    Sounds like it can't find all the headers - log and exp are in math.h which the author has included in ranmath.h. Presumably you aren't a C programmer?
    Not at all.
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    Quote Originally Posted by anglesqueville View Post
    Not at all.
    Sorry, I rewrote that after you quoted me and it was for bas who I've pmd. But UNIX and C are so intertwined its commonly assumed if you are using one you know the other. Usually make fails due to not finding headers or libraries.
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    Just gave this a shot on my laptop which is running Fedora Rawhide (eg. what is basically going to be Fedora 28)
    [[email protected] src]$ cat /etc/redhat-release
    Fedora release 28 (Rawhide)
    [[email protected] src]$ uname -a
    Linux lugh 4.14.0-0.rc2.git3.1.fc28.x86_64 #1 SMP Thu Sep 28 18:41:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
    [[email protected] src]$
    [[email protected] AdmixTools-master]$ cd src
    [[email protected] src]$ make clobber
    rm -f *.o
    rm -f *junk*
    rm -f core
    make -C nicksrc clean
    make[1]: Entering directory '/home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/nicksrc'
    rm -f *.o
    rm -f libnick.a
    make[1]: Leaving directory '/home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/nicksrc'
    rm -f qp3Pop qpDstat qpF4ratio qpAdm qpWave rolloff convertf dowtjack expfit.sh grabpars qpBound qpGraph qpreroot qpff3base rolloffp qpDpart
    rm -rf /home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/admixtables
    rm -f tables
    rm -f ../bin/*
    [[email protected] src]$ make install
    make -C nicksrc
    make[1]: Entering directory '/home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/nicksrc'
    cc -c -g -p -Wimplicit -I./ -c -o strsubs.o strsubs.c
    cc -c -g -p -Wimplicit -I./ -c -o sortit.o sortit.c
    cc -c -g -p -Wimplicit -I./ -c -o vsubs.o vsubs.c
    cc -c -g -p -Wimplicit -I./ -c -o statsubs.o statsubs.c
    cc -c -g -p -Wimplicit -I./ -c -o linsubs.o linsubs.c
    cc -c -g -p -Wimplicit -I./ -c -o getpars.o getpars.c
    cc -c -g -p -Wimplicit -I./ -c -o xsearch.o xsearch.c
    cc -c -g -p -Wimplicit -I./ -c -o gauss.o gauss.c
    cc -c -g -p -Wimplicit -I./ -c -o gds.o gds.c
    ar -r libnick.a strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o gds.o
    ar: creating libnick.a
    ranlib libnick.a
    make[1]: Leaving directory '/home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/nicksrc'
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qp3Pop.o qp3Pop.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpsubs.o qpsubs.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o mcio.o mcio.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o ldsubs.o ldsubs.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o admutils.o admutils.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o egsubs.o egsubs.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o regsubs.o regsubs.c
    cc -L./nicksrc qp3Pop.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qp3Pop
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpDstat.o qpDstat.c
    cc -L./nicksrc qpDstat.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpDstat
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpF4ratio.o qpF4ratio.c
    cc -L./nicksrc qpF4ratio.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpF4ratio
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpAdm.o qpAdm.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o f4rank.o f4rank.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o eigsubs.o eigsubs.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o eigx.o eigx.c
    cc -L./nicksrc qpAdm.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o f4rank.o eigsubs.o eigx.o -lgsl -lopenblas -lm -lnick -o qpAdm
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpWave.o qpWave.c
    cc -L./nicksrc qpWave.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o f4rank.o eigsubs.o eigx.o -lgsl -lopenblas -lm -lnick -o qpWave
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o rolloff.o rolloff.c
    cc -L./nicksrc rolloff.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o rolloff
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o convertf.o convertf.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o h2d.o h2d.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o exclude.o exclude.c
    cc -L./nicksrc convertf.o nicksrc/libnick.a mcio.o admutils.o egsubs.o h2d.o exclude.o -lgsl -lopenblas -lm -lnick -o convertf
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o dowtjack.o dowtjack.c
    cc -L./nicksrc dowtjack.o nicksrc/libnick.a -lgsl -lopenblas -lm -lnick -o dowtjack
    sed -e "s&BBBIN&/home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/../bin&" < expfit.templ > expfit.sh
    chmod +x expfit.sh
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o grabpars.o grabpars.c
    cc -L./nicksrc grabpars.o nicksrc/libnick.a -lgsl -lopenblas -lm -lnick -o grabpars
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpBound.o qpBound.c
    cc -L./nicksrc qpBound.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpBound
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpGraph.o qpGraph.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o gslqp.o gslqp.c
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpgsubs.o qpgsubs.c
    cc -L./nicksrc qpGraph.o nicksrc/libnick.a gslqp.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpGraph
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpreroot.o qpreroot.c
    cc -L./nicksrc qpreroot.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpreroot
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpff3base.o qpff3base.c
    cc -L./nicksrc qpff3base.o nicksrc/libnick.a qpgsubs.o qpsubs.o mcio.o admutils.o egsubs.o regsubs.o ldsubs.o -lgsl -lopenblas -lm -lnick -o qpff3base
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o rolloffp.o rolloffp.c
    rolloffp.c: In function ‘cntit1’:
    rolloffp.c:789:23: warning: ‘return’ with no value, in function returning non-void
    if (cupt -> ignore) return ;
    ^~~~~~
    rolloffp.c:783:8: note: declared here
    double cntit1(double *xc, SNP *cupt, Indiv **indm, int numindivs, int t)
    ^~~~~~
    rolloffp.c: In function ‘cntit2’:
    rolloffp.c:808:23: warning: ‘return’ with no value, in function returning non-void
    if (cupt -> ignore) return ;
    ^~~~~~
    rolloffp.c:802:8: note: declared here
    double cntit2(double *xc, SNP *cupt, SNP *cupt2, Indiv **indm, int numindivs, int t)
    ^~~~~~
    rolloffp.c:809:24: warning: ‘return’ with no value, in function returning non-void
    if (cupt2 -> ignore) return ;
    ^~~~~~
    rolloffp.c:802:8: note: declared here
    double cntit2(double *xc, SNP *cupt, SNP *cupt2, Indiv **indm, int numindivs, int t)
    ^~~~~~
    cc -L./nicksrc rolloffp.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o rolloffp
    cc -c -g -p -Wimplicit -I./ -I./nicksrc -c -o qpDpart.o qpDpart.c
    cc -L./nicksrc qpDpart.o nicksrc/libnick.a qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o -lgsl -lopenblas -lm -lnick -o qpDpart
    mkdir -p /home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/admixtables
    echo "tables made" > tables
    cp twtable /home/dubhthach/Downloads/AdmixTools/AdmixTools-master/src/admixtables
    mkdir -p ../bin
    cp qp3Pop qpDstat qpF4ratio qpAdm qpWave rolloff convertf dowtjack expfit.sh grabpars qpBound qpGraph qpreroot qpff3base rolloffp qpDpart ../bin
    cp rexpfit.r wtjack.pl ../bin
    [[email protected] src]$ ls -lh ../bin
    total 7.8M
    -rwxrwxr-x. 1 dubhthach dubhthach 429K Oct 2 21:25 convertf
    -rwxrwxr-x. 1 dubhthach dubhthach 262K Oct 2 21:25 dowtjack
    -rwxrwxr-x. 1 dubhthach dubhthach 1.7K Oct 2 21:25 expfit.sh
    -rwxrwxr-x. 1 dubhthach dubhthach 145K Oct 2 21:25 grabpars
    -rwxrwxr-x. 1 dubhthach dubhthach 564K Oct 2 21:25 qp3Pop
    -rwxrwxr-x. 1 dubhthach dubhthach 612K Oct 2 21:25 qpAdm
    -rwxrwxr-x. 1 dubhthach dubhthach 569K Oct 2 21:25 qpBound
    -rwxrwxr-x. 1 dubhthach dubhthach 564K Oct 2 21:25 qpDpart
    -rwxrwxr-x. 1 dubhthach dubhthach 580K Oct 2 21:25 qpDstat
    -rwxrwxr-x. 1 dubhthach dubhthach 569K Oct 2 21:25 qpF4ratio
    -rwxrwxr-x. 1 dubhthach dubhthach 636K Oct 2 21:25 qpff3base
    -rwxrwxr-x. 1 dubhthach dubhthach 674K Oct 2 21:25 qpGraph
    -rwxrwxr-x. 1 dubhthach dubhthach 608K Oct 2 21:25 qpreroot
    -rwxrwxr-x. 1 dubhthach dubhthach 595K Oct 2 21:25 qpWave
    -rw-rw-r--. 1 dubhthach dubhthach 4.7K Oct 2 21:25 rexpfit.r
    -rwxrwxr-x. 1 dubhthach dubhthach 572K Oct 2 21:25 rolloff
    -rwxrwxr-x. 1 dubhthach dubhthach 571K Oct 2 21:25 rolloffp
    -rwxr-xr-x. 1 dubhthach dubhthach 2.4K Oct 2 21:25 wtjack.pl
    Some warnings but it basically built it without any issues, now if I recall I had built this before when the laptop was on Fedora 25, as I had done a 'upgrade' to dev release (eg. rawhide) it's probable I already had all the various component packages (rpm's) installed.
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     Bas (10-02-2017)

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    Quote Originally Posted by MacUalraig View Post
    Sorry, I rewrote that after you quoted me and it was for bas who I've pmd. But UNIX and C are so intertwined its commonly assumed if you are using one you know the other. Usually make fails due to not finding headers or libraries.
    OK. I told that I was not (at all) a C programmer, but it's not quite true. I'm mainly too lasy for C. About admixtools, that worked for me (on fedora25) after I had installed lapack, blas and openblas. That said I seem to recall that the linux executables of qpAdm, qpDstat etc are directly downloadable on github. Bas may try to download them and simply copy them in the directory of admixtools, right?
    edit: incidentally, the "thanks" icon is missing at the end of the last post. So... thanks Dubhthach
    Last edited by anglesqueville; 10-02-2017 at 08:38 PM.
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    Quote Originally Posted by anglesqueville View Post
    I don't want to be pessimistic, but I was quite unable to install admixtools on ubuntu, mint, even scientific linux. I had problems with the version of the compilater. That said, make sure you have the following biblios ( openblas and lapack):

    openblas-threads64_-0.2.19-4.el7.x86_64
    openblas-serial64_-0.2.19-4.el7.x86_64
    openblas-openmp64-0.2.19-4.el7.x86_64
    openblas-openmp-0.2.19-4.el7.x86_64
    openblas-threads-0.2.19-4.el7.x86_64
    openblas-threads64-0.2.19-4.el7.x86_64
    openblas-0.2.19-4.el7.x86_64
    openblas-openmp64_-0.2.19-4.el7.x86_64
    openblas-serial64-0.2.19-4.el7.x86_64
    openblas-devel-0.2.19-4.el7.x86_64
    openblas-static-0.2.19-4.el7.x86_64
    openblas-Rblas-0.2.19-4.el7.x86_64
    blas-devel-3.4.2-5.el7.x86_64
    lapack-devel-3.4.2-5.el7.x86_64
    lapack64-3.4.2-5.el7.x86_64
    blas64-3.4.2-5.el7.x86_64
    blas64-devel-3.4.2-5.el7.x86_64
    lapack64-devel-3.4.2-5.el7.x86_64
    lapack64-static-3.4.2-5.el7.x86_64
    lapack-static-3.4.2-5.el7.x86_64
    Thanks, I actually just tried to get it to build on Fedora 25 as per what Dubhthach did in this thread: http://www.anthrogenica.com/showthre...p-Ubuntu/page2

    It gave me the following error messages saying that it cannot find -llapack and -lblas which are the files that you just mentioned.

    What would the commands be to download all of the files you mentioned? Can I write a command to download all of them at once? I've also attached a pic of what I gotIMG_20171002_121550.jpg

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