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Bio-MUST-Drivers-0.191910
River stage one • 4 direct dependents • 4 total dependents

Changes for version 0.191910 - 2019-07-10

  • Additions
    • all: now try to install external dependencies using Homebrew
    • Cap3: added support for optional args to constructor
    • CdHit: added autoselection of cd-hit-est for nt seqs
  • Changes
    • all: improved warning and error messages (now prefixed by [BMD])
    • Blast: now explicitly requires perl-5.18
  • Fixes
    • Hmmer: updated tests to HMMER 3.2.1
    • Cap3: fixed inconsistent contig names between seqs and clusters

Modules

Bio::MUST::Drivers
Bio::MUST classes for driving external programs
Bio::MUST::Drivers::Blast
Bio::MUST driver for running the NCBI-BLAST+ suite of programs
Bio::MUST::Drivers::Blast::Database
Internal class for BLAST driver
Bio::MUST::Drivers::Blast::Database::Temporary
Internal class for BLAST driver
Bio::MUST::Drivers::Cap3
Bio::MUST driver for running the CAP3 assembly program
Bio::MUST::Drivers::CdHit
Bio::MUST driver for running the CD-HIT program
Bio::MUST::Drivers::ClustalO
Bio::MUST driver for running the Clustal Omega program
Bio::MUST::Drivers::Exonerate
Bio::MUST driver for running the Exonerate alignment program
Bio::MUST::Drivers::Exonerate::Aligned
Bio::MUST driver for running the exonerate alignment program
Bio::MUST::Drivers::Exonerate::Sugar
Internal class for exonerate driver
Bio::MUST::Drivers::Hmmer
Bio::MUST driver for running HMMER3
Bio::MUST::Drivers::Hmmer::Model
Internal class for HMMER3 driver
Bio::MUST::Drivers::Hmmer::Model::Database
Internal class for HMMER3 driver
Bio::MUST::Drivers::Hmmer::Model::Temporary
Internal class for HMMER3 driver
Bio::MUST::Drivers::Mafft
Bio::MUST driver for running the MAFFT program
Bio::MUST::Drivers::Roles::Blastable
BLAST database-related methods
Bio::MUST::Drivers::Roles::Hmmerable
HMMER model-related methods
Bio::MUST::Drivers::Utils
Utility functions for drivers
Bio::MUST::Provision::Blast
Internal class for app provisioning system
Bio::MUST::Provision::Cap3
Internal class for app provisioning system
Bio::MUST::Provision::CdHit
Internal class for app provisioning system
Bio::MUST::Provision::ClustalO
Internal class for app provisioning system
Bio::MUST::Provision::Exonerate
Internal class for app provisioning system
Bio::MUST::Provision::Hmmer
Internal class for app provisioning system
Bio::MUST::Provision::Mafft
Internal class for app provisioning system

Other files