Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run bam2cfg.pl
2
gravatar for johnnytam100
2.1 years ago by
johnnytam100 • 100
johnnytam100 • 100 wrote:

My command is as follows :

/data/tam/script/breakdancer-test-compile/lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl bwa1/bam/TTNR_bam_0-1000/libTTNRgenome_master_aln.bam.tmp.0000.bam

However, the error as follows appeared :

Can't locate Statistics/Descriptive.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /data/tam/script/breakdancer-test-compile/lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl line 7. BEGIN failed--compilation aborted at /data/tam/script/breakdancer-test-compile/lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl line 7.

I have read similar post related to adding path to INC but still didn't work.

Any idea what to do? Since I am quite new to linux, explaining from the basics would be much appreciated.

Thanks in advance.
inc bam2cfg.pl breakdancer perl • 2.5k views
ADD COMMENT • link •
modified 2.1 years ago by amy.bashir • 80 • written 2.1 years ago by johnnytam100 • 100
2
gravatar for amy.bashir
2.1 years ago by
amy.bashir • 80
amy.bashir • 80 wrote:

I remember having a similar problem, it was because I had two versions of Perl installed so the paths got all messed up.

Is the Statistics/Descriptive module in one of the paths listed in @INC: /usr/local/lib64/perl5 OR /usr/local/share/perl5 OR /usr/lib64/perl5/vendor_perl OR /usr/share/perl5/vendor_perl OR /usr/lib64/perl5 /usr/share/perl5 ?

You can use perldoc to locate where you installed the Statistics/Descriptive module

perldoc -lm Statistics::Descriptive
ADD COMMENT • link written 2.1 years ago by amy.bashir • 80

I tried... and the result is 

No module found for "Statistics::Descriptive".

And I am trying to install Statistics-Descriptive-3.0612 now but another error said I don't have permission to write...

ERROR: Can't create '/usr/local/share/man/man3'
Do not have write permissions on '/usr/local/share/man/man3'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /usr/share/perl5/Module/Build/Base.pm line 2988

There is little info about this situation on google. Do you know how could I write or somehow install to another directory?

Thank you!

ADD REPLY • link modified 2.1 years ago • written 2.1 years ago by johnnytam100 • 100
1

I will just say up front that I am really new to all this too...

Do you have root access on the system you are using, i.e. can you use sudo?

Maybe it would be easier to follow the instructions here to set up a new place where you can use CPANminus to install modules.

ADD REPLY • link written 2.1 years ago by amy.bashir • 80

It worked!!! Thank you very much!!!

ADD REPLY • link written 2.1 years ago by johnnytam100 • 100
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1341 users visited in the last hour