VAAST (Variant Annotation, Analysis and Search Tool)
1
0
Entering edit mode
5.3 years ago
nudrylab • 0

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

software error gene next-gen • 946 views
ADD COMMENT
0
Entering edit mode

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
ADD REPLY
1
Entering edit mode
5.3 years ago
Brice Sarver ★ 3.8k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1543 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6