Jennifer-1991
commented
2 years ago I am not a programmer, but have been attempting and facing the same problem. During extensive internet search, I found this
export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/
and afterwards if you run
roary -h
it works. You can try it.
According to the solution you suggested, I run the $ cpanm -f Bio::Roary and some modules are not installed. Here is the information.
--> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.13.0.tar.gz ... OK Configuring Bio-Roary-3.13.0 ... OK ==> Found dependencies: Bio::Perl, Bio::TreeIO, Bio::Tools::GFF, Bio::SeqIO --> Working on Bio::Perl Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz ... OK Configuring Bio-Procedural-1.7.4 ... OK ==> Found dependencies: Bio::Root::Version, Bio::DB::GenPept, Bio::DB::RefSeq, Bio::Seq, Bio::SeqIO, Bio::DB::EMBL, Bio::DB::GenBank, Bio::Root::Test, Bio::DB::SwissProt, Bio::Tools::Run::RemoteBlast --> Working on Bio::Root::Version Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz ... OK Configuring BioPerl-1.7.8 ... OK ==> Found dependencies: DB_File --> Working on DB_File Fetching http://www.cpan.org/authors/id/P/PM/PMQS/DB_File-1.857.tar.gz ... OK Configuring DB_File-1.857 ... OK Building and testing DB_File-1.857 ... FAIL ! Installing DB_File failed. See /home/cheyanlin/.cpanm/work/1648866949.1199618/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'DB_File' is not installed ! Bailing out the installation for BioPerl-1.7.8. --> Working on Bio::DB::GenPept Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz ... OK Configuring Bio-DB-NCBIHelper-1.7.7 ... OK ==> Found dependencies: Bio::Taxon, Bio::SeqIO, Bio::Root::Root, Bio::Root::IO, Bio::DB::Query::WebQuery, Bio::DB::WebDBSeqI, Bio::SeqIO::entrezgene, Bio::DB::Taxonomy, Bio::WebAgent, Cache::FileCache --> Working on Bio::SeqIO::entrezgene Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-ASN1-EntrezGene-1.73.tar.gz ... OK Configuring Bio-ASN1-EntrezGene-1.73 ... OK ==> Found dependencies: Bio::SeqIO, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Root::Test, Bio::SeqFeature::Gene::Transcript, Bio::SeqFeature::Gene::Exon, Bio::Annotation::SimpleValue, Bio::SeqFeature::Gene::GeneStructure, Bio::Cluster::SequenceFamily, Bio::Annotation::OntologyTerm, Bio::SeqFeature::Generic, Bio::Species, Bio::Annotation::Reference, Bio::Seq, Bio::Index::AbstractSeq, Bio::Ontology::Term --> Working on Bio::Cluster::SequenceFamily Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Cluster-1.7.3.tar.gz ... OK Configuring Bio-Cluster-1.7.3 ... OK ==> Found dependencies: Bio::IdentifiableI, Bio::Root::Root, Bio::Variation::SNP, Bio::Factory::SequenceStreamI, Bio::Root::Test, Bio::Factory::ObjectFactory, Bio::Annotation::DBLink, Bio::AnnotatableI, Bio::Annotation::SimpleValue, Bio::DescribableI, Bio::Species, Bio::Root::IO, Bio::Seq::SeqFactory, Bio::Annotation::Collection, Bio::Root::RootI --> Working on Bio::Variation::SNP Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Variation-1.7.5.tar.gz ... OK Configuring Bio-Variation-1.7.5 ... OK ==> Found dependencies: Bio::PrimarySeq, Bio::DBLinkContainerI, Bio::Root::IO, Bio::SeqFeature::Generic, Bio::Root::Test, Bio::Root::Root, Bio::Tools::CodonTable, Bio::SeqIO ! Installing the dependencies failed: Module 'Bio::SeqFeature::Generic' is not installed, Module 'Bio::DBLinkContainerI' is not installed, Module 'Bio::PrimarySeq' is not installed, Module 'Bio::Root::IO' is not installed, Module 'Bio::Tools::CodonTable' is not installed, Module 'Bio::Root::Root' is not installed, Module 'Bio::SeqIO' is not installed, Module 'Bio::Root::Test' is not installed ! Bailing out the installation for Bio-Variation-1.7.5. ! Installing the dependencies failed: Module 'Bio::Seq::SeqFactory' is not installed, Module 'Bio::Annotation::Collection' is not installed, Module 'Bio::Root::RootI' is not installed, Module 'Bio::Root::IO' is not installed, Module 'Bio::Species' is not installed, Module 'Bio::Variation::SNP' is not installed, Module 'Bio::Root::Root' is not installed, Module 'Bio::Factory::SequenceStreamI' is not installed, Module 'Bio::IdentifiableI' is not installed, Module 'Bio::DescribableI' is not installed, Module 'Bio::Annotation::SimpleValue' is not installed, Module 'Bio::Root::Test' is not installed, Module 'Bio::Annotation::DBLink' is not installed, Module 'Bio::AnnotatableI' is not installed, Module 'Bio::Factory::ObjectFactory' is not installed ! Bailing out the installation for Bio-Cluster-1.7.3. ! Installing the dependencies failed: Module 'Bio::Cluster::SequenceFamily' is not installed, Module 'Bio::SeqFeature::Generic' is not installed, Module 'Bio::Annotation::OntologyTerm' is not installed, Module 'Bio::SeqFeature::Gene::GeneStructure' is not installed, Module 'Bio::Seq' is not installed, Module 'Bio::Annotation::Reference' is not installed, Module 'Bio::Ontology::Term' is not installed, Module 'Bio::Index::AbstractSeq' is not installed, Module 'Bio::Species' is not installed, Module 'Bio::Annotation::Comment' is not installed, Module 'Bio::SeqIO' is not installed, Module 'Bio::SeqFeature::Gene::Exon' is not installed, Module 'Bio::Annotation::SimpleValue' is not installed, Module 'Bio::SeqFeature::Gene::Transcript' is not installed, Module 'Bio::Annotation::DBLink' is not installed, Module 'Bio::Root::Test' is not installed ! Bailing out the installation for Bio-ASN1-EntrezGene-1.73. --> Working on Cache::FileCache Fetching http://www.cpan.org/authors/id/R/RJ/RJBS/Cache-Cache-1.08.tar.gz ... OK Configuring Cache-Cache-1.08 ... OK ==> Found dependencies: Digest::SHA1 --> Working on Digest::SHA1 Fetching http://www.cpan.org/authors/id/G/GA/GAAS/Digest-SHA1-2.13.tar.gz ... OK Configuring Digest-SHA1-2.13 ... OK Building and testing Digest-SHA1-2.13 ... FAIL ! Installing Digest::SHA1 failed. See /home/cheyanlin/.cpanm/work/1648866949.1199618/build.log for details. Retry with --force to force install it. ! Installing the dependencies failed: Module 'Digest::SHA1' is not installed ! Bailing out the installation for Cache-Cache-1.08. ! Installing the dependencies failed: Module 'Bio::SeqIO' is not installed, Module 'Bio::Root::Root' is not installed, Module 'Bio::Taxon' is not installed, Module 'Bio::SeqIO::entrezgene' is not installed, Module 'Bio::DB::WebDBSeqI' is not installed, Module 'Cache::FileCache' is not installed, Module 'Bio::DB::Taxonomy' is not installed, Module 'Bio::WebAgent' is not installed, Module 'Bio::Root::IO' is not installed, Module 'Bio::DB::Query::WebQuery' is not installed ! Bailing out the installation for Bio-DB-NCBIHelper-1.7.7. --> Working on Bio::DB::RefSeq Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-RefSeq-1.7.4.tar.gz ... OK Configuring Bio-DB-RefSeq-1.7.4 ... OK ==> Found dependencies: Bio::DB::DBFetch ! Installing the dependencies failed: Module 'Bio::DB::DBFetch' is not installed ! Bailing out the installation for Bio-DB-RefSeq-1.7.4. --> Working on Bio::DB::EMBL Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-EMBL-1.7.4.tar.gz ... OK Configuring Bio-DB-EMBL-1.7.4 ... OK ==> Found dependencies: Bio::DB::DBFetch ! Installing the dependencies failed: Module 'Bio::DB::DBFetch' is not installed ! Bailing out the installation for Bio-DB-EMBL-1.7.4. --> Working on Bio::DB::SwissProt Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-SwissProt-1.7.4.tar.gz ... OK Configuring Bio-DB-SwissProt-1.7.4 ... OK ==> Found dependencies: Bio::DB::WebDBSeqI ! Installing the dependencies failed: Module 'Bio::DB::WebDBSeqI' is not installed ! Bailing out the installation for Bio-DB-SwissProt-1.7.4. --> Working on Bio::Tools::Run::RemoteBlast Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Tools-Run-RemoteBlast-1.7.3.tar.gz ... OK Configuring Bio-Tools-Run-RemoteBlast-1.7.3 ... OK ==> Found dependencies: Bio::SeqIO, Bio::Root::IO, Bio::Root::Version, Bio::SearchIO ! Installing the dependencies failed: Module 'Bio::SeqIO' is not installed, Module 'Bio::Root::IO' is not installed, Module 'Bio::Root::Version' is not installed, Module 'Bio::SearchIO' is not installed ! Bailing out the installation for Bio-Tools-Run-RemoteBlast-1.7.3. ! Installing the dependencies failed: Module 'Bio::Tools::Run::RemoteBlast' is not installed, Module 'Bio::DB::GenBank' is not installed, Module 'Bio::Root::Test' is not installed, Module 'Bio::DB::SwissProt' is not installed, Module 'Bio::DB::EMBL' is not installed, Module 'Bio::SeqIO' is not installed, Module 'Bio::Seq' is not installed, Module 'Bio::DB::RefSeq' is not installed, Module 'Bio::DB::GenPept' is not installed, Module 'Bio::Root::Version' is not installed ! Bailing out the installation for Bio-Procedural-1.7.4. ! Installing the dependencies failed: Module 'Bio::SeqIO' is not installed, Module 'Bio::Perl' is not installed, Module 'Bio::TreeIO' is not installed, Module 'Bio::Tools::GFF' is not installed ! Bailing out the installation for Bio-Roary-3.13.0.
What is the matter? Thank you very much. Looking forward to your reply.