sh: smartpca: command not found

[montenegrina]

Hello,

I downloaded in the current directory from where I am running smartpca.perl that script and evec2pca-ped.perl

I was running:
perl smartpca.perl -i output5F.bed -a output5F.pedsnp -b output5F.pedind -o output5F.pca -p output5F.plot -e output5F.eval -l output5F.smart
pca.log -m 5 -k 3 -t 2
smartpca -p output5F.pca.par >output5F.smartpca.log
sh: smartpca: command not found
OOPS couldn't open file output5F.pca.evec for reading at smartpca.perl line 65.

Can you please tell me how to resolve this?

I made both scripts executable via:
chmod a+x evec2pca-ped.perl
chmod a+x smartpca.perl

Please advise,
Thanks

[montenegrina]

I also tried to add to the $PATH where both .perl scripts are:
export PATH="/projects/com_grassim/anamaria/anamaria/anamaria/dbgap_gokind/69568/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output3:$PATH"

but again the same error

[MatthewMah]

Did you build the smartpca executable?

[montenegrina]

no I just downloaded smartpca.perl and evec2pca-ped.perl

How do I build this?

[montenegrina]

I am running this on Ubuntu cluster

[montenegrina]

I did try to install it from source in /src but after running "make" I got this:

$ make
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o baseprog.o baseprog.c
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o mcio.o mcio.c
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o egsubs.o egsubs.c
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o admutils.o admutils.c
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o h2d.o h2d.c
cc -I/software/linux-el7-x86_64/tools/gtc2vcf/include -I../include -I/usr/include/openblas -c -o eigensrc/exclude.o eigensrc/exclude.c
make -C nicksrc
make[1]: Entering directory /projects/com_grassim/anamaria/anamaria/anamaria/dbgap_gokind/69568/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output3/EIG/src/nicksrc' cc -I../../include -D_GNU_SOURCE -c -o gauss.o gauss.c cc -I../../include -D_GNU_SOURCE -c -o gds.o gds.c cc -I../../include -D_GNU_SOURCE -c -o getpars.o getpars.c cc -I../../include -D_GNU_SOURCE -c -o linsubs.o linsubs.c cc -I../../include -D_GNU_SOURCE -c -o sortit.o sortit.c cc -I../../include -D_GNU_SOURCE -c -o statsubs.o statsubs.c cc -I../../include -D_GNU_SOURCE -c -o strsubs.o strsubs.c cc -I../../include -D_GNU_SOURCE -c -o vsubs.o vsubs.c cc -I../../include -D_GNU_SOURCE -c -o xsearch.o xsearch.c cc -I../../include -D_GNU_SOURCE -c -o twtable.o twtable.c ar -r libnick.a gauss.o gds.o getpars.o linsubs.o sortit.o statsubs.o strsubs.o vsubs.o xsearch.o twtable.o ar: creating libnick.a make[1]: Leaving directory /projects/com_grassim/anamaria/anamaria/anamaria/dbgap_gokind/69568/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output3/EIG/src/nicksrc'
cc -L/software/linux-el7-x86_64/tools/gtc2vcf/lib baseprog.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o baseprog
/usr/bin/ld: cannot find -lopenblas
collect2: error: ld returned 1 exit status
make: *** [baseprog] Error 1

[MatthewMah]

First, you have to install gsl and and openblas. The commands should be something like:

sudo apt-get install gsl-dev
sudo apt-get install openblas-dev

I don't have an Ubuntu machine available to verify these are correct. The package names may be different.

Once these are installed, try to run "make". If this fails, then you need to tell the linker where to find the gsl and openblas libraries. You can do this on the command line with something like:

make LDFLAGS="-L/usr/local/opt/openblas/lib -L/usr/local/opt/gsl/lib"

Or you can modify the Makefile.

I don't know where these libraries will be located on your machine, so the above paths are simply examples. You can find them using the standard utility find with something like:

find / "libgsl*"