VAAST (Variant Annotation, Analysis and Search Tool)

Question

[nudrylab]

Hello, I have been trying to install VAAST on my computer and I was not able. On my MAC I am receiving this message:

Please check, if the URLs I found in your configuration file
(http://cpan.netnitco.net/, http://cpan.mirror.clemson.edu/,
http://soft-download.org/) are valid. The urllist can be edited. E.g. with
'o conf urllist push ftp://myurl/'
Could not fetch authors/01mailrc.txt.gz
  

I have tried to install it on Linux as well, and on Linux, I am getting these errors:

Ubuntu:~/Desktop/VAAST_Code_2.2.0/$ perl Build.PL

        Can't open perl script "Build.PL": No such file or directory
  

Ubuntu:~/Desktop/VAAST_Code_2.2.0/$ perl --version

This is perl 5, version 26, subversion 1 (v5.26.1) build for x86_64-linux-gnu-thread-multi
...
  

Can anyone help me with this problem?

Thank you

[nudrylab]

I have tried to follow the instructions that were provided and I was not able to make it work.

VAAST Quick Install:

  ---------------------------------------- COMMAND LINE ----------------------------------------
   perl Build.PL
   sudo ./Build installdeps
   ./Build test
   ./Build install
   # To use covariant adjusted permutation install the R BiasedUrn package:
   # Check for latest version: https://cran.r-project.org/web/packages/BiasedUrn/index.html
   wget https://cran.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz
   tar -xzvf BiasedUrn_1.07.tar.gz
   R CMD INSTALL BiasedUrn

Answer 1

[Brice Sarver]

Likely off-topic for Biostars. More suited to Stack Overflow.

I will mention that your perl call on Linux is simply telling you that 'Build.PL' doesn't exist in your working directory. build.pl/Build.pl/Build.PL/build.PL matter here. I'd recommend following an introductory tutorial for the MacOS/Linux command line.