bioperl/bioperl-run

Issues

• t/SABlastPlus.t failures with makeblastdb from ncbi-blast+ 2.16.0

  #62 opened 4 months ago by emollier
  0

• Where to acquire Helicobacter_pylori.mod needed by t/Genemark.hmm.prokaryotic.t ?

  #60 opened 5 years ago by mr-c
  0

• Bug in Eponine test

  #59 opened 6 years ago by dionys
  0

• BEDTools issues

  #58 opened 6 years ago by cjfields
  0

• Build.PL mentions `Bio::Run` that does not exist

  #57 opened 6 years ago by carandraug
  2

• Perl

  #56 opened 6 years ago by AmitaCM
  1

• Issue with Bowtie in test suite

  #55 opened 7 years ago by tillea
  1

• bug in Bio::Tools::Run::Alignment::StandAloneFasta

  #53 opened 7 years ago by cjfields
  0

• Test with latest bowtie is failing

  #52 opened 7 years ago by tillea
  0

• infernal does not contan cmscore since version 1.1

  #45 opened 8 years ago by tillea
  1

• Index on cpanm?

  #41 opened 8 years ago by keiranmraine
  1

• SABlastPlus tests fail with latest version of BLAST+

  #51 opened 7 years ago by cjfields
  0

• Codeml (v 4v4d) using fixed kappa value, reports wrong kappa

  #35 opened 7 years ago by cjfields
  3

• Bio::Tools::Run::StandAloneBlastPlus HTML output

  #48 opened 8 years ago by bretonics
  4

• qualifiers for for water/needle@ Bio::Factory::EMBOSS

  #50 opened 8 years ago by rafalcode
  5

• 'cpgplot' input sequence not recognized

  #47 opened 8 years ago by piatekmj
  9

• Bio::Factory::EMBOSS dies on OSX when checking for operating system

  #46 opened 8 years ago by piatekmj
  5

• Bio::Tools::Run::Phylo::Phyml use default parameter for interleaved input, but it use sequential input

  #43 opened 8 years ago by qifei9
  1

• Bio::Tools::Run::Phylo::Phyml, rand_starts cannot be set to 0

  #44 opened 8 years ago by qifei9
  1

• Tests fail when command is not installed.

  #11 opened 8 years ago by hartzell
  9

• DB can't be found

  #37 opened 8 years ago by ksteczk
  1

• problem in Installing Bio::Seq, Bio::DB::GFF,

  #36 opened 9 years ago by amoltej
  6

• Bio::Tools::Run::StandAloneBlastPlus --remote database with '/' separator

  #34 opened 9 years ago by cjfields
  1

• Bio::Tools::Run::Phylo::Phyml, tree_string

  #33 opened 9 years ago by cjfields
  0

• Undocumented need for Array::Compare.

  #32 opened 9 years ago by cjfields
  2

• Bio::Tools::Run::Phylo::Phyml Lacks LG model of AA sequence evolution

  #31 opened 9 years ago by cjfields
  0

• version() not implemented for Bio::Tools::Run::StandAloneBlastPlus

  #30 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::StandAloneBlastPlus tests failing with latest BLAST+

  #29 opened 9 years ago by cjfields
  3

• Bio::Tools::Run::BWA failing tests

  #28 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::Phylo::Phyml -- documented values for -f parameter

  #27 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::Phylo::Phyml -- Bootstrap and other confidence measures

  #26 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::StandAloneBlastPlus "entrez_query" option

  #25 opened 9 years ago by cjfields
  3

• bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3

  #24 opened 9 years ago by cjfields
  2

• -task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus

  #23 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters

  #22 opened 9 years ago by cjfields
  1

• Bio::Tools::Run::Genewise doesn't accept parameters as described in its documentation

  #21 opened 9 years ago by cjfields
  0

• Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above

  #20 opened 9 years ago by cjfields
  3

• ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail

  #19 opened 9 years ago by cjfields
  1

• Add Amap, Kalign and Probcon Quiet option

  #18 opened 9 years ago by cjfields
  2

• mumsa wrapper

  #17 opened 9 years ago by cjfields
  1

• Implement a seqgen wrapper in bioperl-run

  #16 opened 9 years ago by cjfields
  1

• Wrappers for ExaML, ExaBayes, *BEAST

  #14 opened 10 years ago by rvosa
  2

• StandAloneBlastPlus can't handle the new multiple-valued -outfmt option

  #12 opened 10 years ago by majensen
  2