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tjparnell / biotoolbox

Tools for querying and analysis of genomic data
http://tjparnell.github.io/biotoolbox/
Artistic License 2.0
27 stars 16 forks source link

Issue on installing Biotoolbox #16

Open marissa97 opened 1 year ago

marissa97 commented 1 year ago

Hello,

I am trying to download Bio::ToolBox It looks like it is now downloaded, however when i run: perl ucsc_table2gff3.pl -f refgene -d hg19 it delivers an error: 

Can't locate Bio/ToolBox.pm in @INC (you may need to install the Bio::ToolBox module) (@INC contains: /home/marissa/miniconda3/lib/perl5/5.32/site_perl /home/marissa/miniconda3/lib/perl5/site_perl /home/marissa/miniconda3/lib/perl5/5.32/vendor_perl /home/marissa/miniconda3/lib/perl5/vendor_perl /home/marissa/miniconda3/lib/perl5/5.32/core_perl /home/marissa/miniconda3/lib/perl5/core_perl .) at ucsc_table2gff3.pl line 9.
BEGIN failed--compilation aborted at ucsc_table2gff3.pl line 9.

Can you please tell me what is wrong ? Thank you!

tjparnell commented 1 year ago

Hello, Based on your error, the package is not installed properly. Did you run the Build script, or go through a Perl package manager such as cpan, cpanm, or cpanp? For more details look at the Advanced Install documentation.

As of this writing, the current version here on GitHub is considerably different (and mostly incompatible) with the released versions on CPAN, but is stable.

The ucsc_table2gff3.pl script is pretty old and I've had to strip out modern incompatibilities. You can also use the get_features.pl script, with the appropriate flags, if you're looking to simply convert annotation formats.