VCFtools installtion error
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Entering edit mode
5.5 years ago

I am trying to install Vcftools and getting this error even after installing the required C compilers.

 

configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
sanjay@sanjay-Inspiron-1545:~/Desktop/vcftools$ sudo make
make  all-recursive
make[1]: Entering directory `/home/sanjay/Desktop/vcftools'
Making all in src
make[2]: Entering directory `/home/sanjay/Desktop/vcftools/src'
Making all in cpp
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src/cpp'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src/cpp'
Making all in perl
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src/perl'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src/perl'
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src'
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools/src'
make[2]: Entering directory `/home/sanjay/Desktop/vcftools'
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools'
make[1]: Leaving directory `/home/sanjay/Desktop/vcftools'
sanjay@sanjay-Inspiron-1545:~/Desktop/vcftools$ sudo make install
Making install in src
make[1]: Entering directory `/home/sanjay/Desktop/vcftools/src'
Making install in cpp
make[2]: Entering directory `/home/sanjay/Desktop/vcftools/src/cpp'
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c vcftools '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/man/man1'
 /usr/bin/install -c -m 644 vcftools.1 '/usr/local/share/man/man1'
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src/cpp'
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools/src/cpp'
Making install in perl
make[2]: Entering directory `/home/sanjay/Desktop/vcftools/src/perl'
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src/perl'
 /bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/perl/5.18.2'
 /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/usr/local/share/perl/5.18.2'
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src/perl'
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools/src/perl'
make[2]: Entering directory `/home/sanjay/Desktop/vcftools/src'
make[3]: Entering directory `/home/sanjay/Desktop/vcftools/src'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/sanjay/Desktop/vcftools/src'
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools/src'
make[1]: Leaving directory `/home/sanjay/Desktop/vcftools/src'
make[1]: Entering directory `/home/sanjay/Desktop/vcftools'
make[2]: Entering directory `/home/sanjay/Desktop/vcftools'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/sanjay/Desktop/vcftools'
make[1]: Leaving directory `/home/sanjay/Desktop/vcftools'

 

please help me to resolve this

vcftools make makeinstall error • 2.2k views
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What is the problem? I don't see anything wrong.

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As far as I can see, the binaries were installed to /usr/local/bin, which should be on your PATH, so you just have to call them. Did you try something like vcf-merge -h?

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