bioperl-run
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bioperl
BioPerl wrappers
On master branch: ``` 16:59 $ ./Build test --test-files t/SABlastPlus.t t/SABlastPlus.t .. 1/73 # DB and mask make tests ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Unknown version output: blastdbcmd: 2.6.0+ Package:...
Session info: perl = v5.22.0 Mac OS = 10.11.6 BioPerl-Run-1.007001 From Bio::Factory::EMBOSS when trying to provide input sequence for `cpgplot` as a variable, I do get an error message saying:...
Hi, I went through my repositories and noticed I had never added the ExaML wrapper that I wrote at the BOSC codefest! The ExaML wrapper looks much like the already...
I have a problem with providing psiblast wrapper with local database. Am I doing anything wrong here? When trying to execute: my $factory = Bio::Tools::Run::StandAloneBlastPlus->new(-db_name => '/db/SEQRES/pdb90.fa'); return $blast_report =...
Hi, I have been trying to install these modules using cpan install command. I have installed all the dependencies and my bioperl installation says it is up to date. But...
--- Author Name: **J Nelson** (J Nelson) Original Redmine Issue: 3322, https://redmine.open-bio.org/issues/3322 Original Date: 2012-02-02 Original Assignee: Bioperl Guts --- The `-remote` parameter to `Bio::Tools::Run::StandAloneBlastPlus->new()` is throwing an error if...
--- Author Name: **Tristan Lefebure** (Tristan Lefebure) Original Redmine Issue: 3273, https://redmine.open-bio.org/issues/3273 Original Date: 2011-07-27 Original Assignee: Bioperl Guts --- Hi there, I am not quite sure I understand why...
--- Author Name: **Charles Plessy** (Charles Plessy) Original Redmine Issue: 3253, https://redmine.open-bio.org/issues/3253 Original Date: 2011-06-18 Original Assignee: Bioperl Guts --- Dear BioPerl developers, BioPerl-Run needs Array::Compare to run its regression...
--- Author Name: **Jessen Bredeson** (Jessen Bredeson) Original Redmine Issue: 3226, https://redmine.open-bio.org/issues/3226 Original Date: 2011-05-02 Original Assignee: Bioperl Guts --- Page 12 of the PhyML 3.0 manual (at http://www.atgc-montpellier.fr/download/papers/phyml\_manual\_2009.pdf) states...
--- Author Name: **Chris Fields** (@cjfields) Original Redmine Issue: 3214, https://redmine.open-bio.org/issues/3214 Original Date: 2011-04-20 Original Assignee: Bioperl Guts --- per subject line. This blocks version-dependent tests.