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bioperl / bioperl-docker

Docker files for BioPerl
Artistic License 2.0
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Bio::ASN1::EntrezGene incorrectly depends on BioPerl v1.7.2 from CPAN #8

Open hlapp opened 6 years ago

hlapp commented 6 years ago

This may be a result of Bio::ASN1:EntrezGene having to be re-released since the change to Dist::Zilla (@cjfields ?), but right now it pulls in BioPerl v1.7.2 from CPAN when installing BioPerl v1.7.3 from source.

Configuring Bio-ASN1-EntrezGene-1.73 ... OK
==> Found dependencies: Bio::Cluster::SequenceFamily
--> Working on Bio::Cluster::SequenceFamily
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... OK
Configuring BioPerl-1.007002 ... OK
Building and testing BioPerl-1.007002 ... OK
Successfully installed BioPerl-1.007002
carandraug commented 6 years ago

This is because Bio-ASN1-Entrezgene distribution is dependent on the Bio::Cluster::SequenceFamily module which has not been released yet. It is part of the Bio-Cluster distribution https://github.com/bioperl/Bio-Cluster/tree/master/lib/Bio

@cjfields I think it will need a new module, Bio::Cluster, so it can be indexed by CPAN, but other than that, it should be ready for release.

carandraug commented 6 years ago

I just followed this through, and Bio-Cluster will be dependent on Bio-Variation. Bio-Variation has a script bp_flanks which requires Bio-DB-EMBL and Bio-DB-NCBIHelper.