[ensembl-dev] prerequisites for Bio-DB-HTS

[Rishi Nag]

Hi Mahmood

You'll need to install Module::Build from CPAN. https://metacpan.org/pod/Module::Build

To install Module::Build, simply copy and paste either of the commands in to your terminal

cpanm

                     cpanm Module::Build
CPAN shell

                     perl -MCPAN -e shell
                     install Module::Build

You should then be able to proceed with the Build.PL step as outlined in the modules.

Regards

Rishi

On 25/06/2017 20:50, Mahmood Naderan wrote:
> The error is
> 
> [mahmood at cluster Bio-DB-HTS]$ perl Build.PL
> Can't locate Module/Build.pm in @INC (@INC contains: /export/home/mahmood/src/bioperl-1.6.1 /export/home/mahmood/src/ensembl/modules 
> /export/home/mahmood/src/ensembl-compara/modules /export/home/mahmood/src/ensembl-variation/modules /export/home/mahmood/src/ensembl-funcgen/modules 
> /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 
> Build.PL line 20.
> BEGIN failed--compilation aborted at Build.PL line 20.
> [mahmood at cluster Bio-DB-HTS]$
> 
> 
> Please see the full output (from the beginning to this step) at https://pastebin.com/PWBiB6fA
> 
> Any thought on that?
> 
> Regards,
> Mahmood
> 
> 
> 
> On Sun, Jun 25, 2017 at 11:40 PM, Mahmood Naderan <mahmood.nt at gmail.com <mailto:mahmood.nt at gmail.com>> wrote:
> 
>     Thanks for the feedback. Meanwhile, I want to know which method is recommended by you for "installing perl packages as non root user". There are
>     some choices including perlbrew, local::lib and other things.
> 
>     I just want to be in the same track as you.
> 
>     Regards,
>     Mahmood
> 
> 
> 
>     On Sun, Jun 25, 2017 at 11:11 PM, Rishi Nag <rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>> wrote:
> 
>         Hi Mahmood
> 
>         The main thing that Bio::DB::HTS depends on that is outside of Perl, so if you could do a ls $HTSLIB_DIR, and some of the error messages, that
>         would be helpful. There are issues on the latest Mac OS that mean the latest HTSlib may not have compiled correctly. If you run 'perl
>         INSTALL.pl' the script will attempt to download and build an earlier HTSlib automatically.
> 
>         You can find further guidance at the readme file for Bio::DB::HTS at https://github.com/Ensembl/Bio-DB-HTS
>         <https://github.com/Ensembl/Bio-DB-HTS>.
> 
>         Regards
> 
>         Rishi
> 
> 
> 
> 
> 
> 
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