bam2cfg.pl not able to find statistics : Breakdancer

Question

[sunnykevin97]

HI, I followed this link Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run bam2cfg.pl It doesn't work for me, how to sort out ?.

 wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib --force
--2018-10-04 21:24:11--  http://cpanmin.us/
Resolving cpanmin.us cpanmin.us)... 151.101.130.217, 151.101.2.217, 151.101.194.217, ...
Connecting to cpanmin.us cpanmin.us)|151.101.130.217|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 302780 (296K) [text/plain]
Saving to: ‘STDOUT’

100%[==================================================================================================================================================================>] 3,02,780    --.-K/s   in 0.02s   

2018-10-04 21:24:11 (18.5 MB/s) - written to stdout [302780/302780]

--> Working on App::cpanminus
Fetching http://www.cpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz ... OK
Configuring App-cpanminus-1.7044 ... OK
Building and testing App-cpanminus-1.7044 ... FAIL
! Installing App::cpanminus failed. See /home/pinn/.cpanm/work/1538668451.38309/build.log for details. Retry with --force to force install it.
--> Working on local::lib
Fetching http://www.cpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz ... OK
Configuring local-lib-2.000024 ... OK
==> Found dependencies: ExtUtils::MakeMaker
--> Working on ExtUtils::MakeMaker
Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/ExtUtils-MakeMaker-7.34.tar.gz ... OK
Configuring ExtUtils-MakeMaker-7.34 ... OK
Building and testing ExtUtils-MakeMaker-7.34 ... FAIL
! Installing ExtUtils::MakeMaker failed. See /home/pinn/.cpanm/work/1538668451.38309/build.log for details. Retry with --force to force install it.
! Installing the dependencies failed: Installed version (6.68) of ExtUtils::MakeMaker is not in range '7.00'
! Bailing out the installation for local-lib-2.000024.

[h.mon]

Read the logs, it should have the cause of the install failure:

less /home/pinn/.cpanm/work/1538668451.38309/build.log

[Nitin Narwade]

The bam2cfg.pl program requires three Perl modules. That has to be installed first on your system.

starting few lines of code taken from bam2cfg.pl

use strict;
use warnings;
use Getopt::Std;
use Statistics::Descriptive;
use GD::Graph::histogram;
use FindBin qw($Bin);
use lib "$FindBin::Bin";
#use lib '/gscuser/kchen/1000genomes/analysis/scripts/';
use AlnParser;

As you mentioned in your question, the error says the system is not able to find out Statistics::Descriptive module, so simply try to install it first with the help of CPAN.

sudo cpan install Statistics::Descriptive

You might get one more error while running this program, which will be concern about GD::Graph module. You need to install it too if it is not there on system.

To Resolve the GD:Graph issue you first have to install GD graph library (Tested on ubuntu 16.04 Server).

sudo apt-get install libgd2-xpm-dev
sudo cpan install GD::Graph::histogram

[Ram]

sudo ...

Nuh-uh, don't suggest sudo unless absolutely required (which is almost always never the case).

[Chris Miller]

My general advice would be to stop using breakdancer. A whole host of more faster, more reliable, and more robust algorithms now exists (manta, lumpy, etc, etc)

[sunnykevin97]

thanks for your suggestion.