Question: Vcftools not running
0
gravatar for pifferdavide
4.7 years ago by
pifferdavide100
Italy
pifferdavide100 wrote:

cd C:/Users/Davide/downloads #set to directory with the tabix package files

tar -xf tabix-0.2.6.tar.bz2 #decompress file

export PERL5LIB=/C:/Users/Davide/vcftools/perl #set the PERL5LIB environment variable to include the vcf.pm module

cd C:/Users/Davide/vcftools #change to the target directory

make #compile the program

cd C:/Users/Davide/vcftools/bin #set directory

 However when I type vcftools, I get this line " Bash: command not found".

cd c:/Users/Davide/vcftools/bin/test.t # I run a test

 

Can't locate Test/Most.pm in @INC (@INC contains: /cygdrive/c/Users/Davide/vcftools/perl /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at c:/Users/Davide/vcftools/perl/test.t line 17.

BEGIN failed--compilation aborted at c:/Users/Davide/vcftools/perl/test.t line 17.

I am using Cygwin from Windows 7A user running Ubuntu 64 bits reported the same error message so I do not think it's got anything to do with Cygwin: see Vcftools, Command Not Found !

 

linux vcftools vcf • 1.7k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by pifferdavide100

I do not think it's anything to do with Test::More. I installed it and it didn't change anything

ADD REPLYlink written 4.7 years ago by pifferdavide100

Can you give me the output of which vcftools please?

ADD REPLYlink written 4.7 years ago by RamRS24k
0
gravatar for RamRS
4.7 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

Your problem is with Test::More not being installed properly. There is no indication that vcftools might be having a problem. You can use CPAN to install Test::More.

perl -MCPAN -e 'install Test::More'

should install Test::More. 

 

ADD COMMENTlink written 4.7 years ago by RamRS24k
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