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Remove -stable from test, it's crashing muscle. Docs say 'THE -stable…
… OPTION HAD A SERIOUS BUG IN VERSIONS OF MUSCLE PRIOR TO v3.8 AND IS CURRENTLY NOT SUPPORTED'
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bosborne committed Sep 19, 2011
1 parent cb0d07c commit 79d30c6
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Showing 2 changed files with 2 additions and 3 deletions.
4 changes: 2 additions & 2 deletions lib/Bio/Tools/Run/Alignment/Muscle.pm
Expand Up @@ -119,15 +119,15 @@ use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase
Bio::Factory::ApplicationFactoryI);


BEGIN {
%DEFAULTS = ( 'AFORMAT' => 'fasta' );
@MUSCLE_PARAMS = qw(IN OUT TREE1 LOG LOGA SCOREFILE GAPOPEN
MAXMB MAXHOURS MAXITERS KBAND IN1 IN2);
MAXMB MAXHOURS MAXITERS KBAND IN1 IN2 USETREE USETREE_NOWARN);
@MUSCLE_SWITCHES = qw(QUIET DIAGS REFINE STABLE GROUP
CLW CLWSTRICT MSF);

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1 change: 0 additions & 1 deletion t/Muscle.t
Expand Up @@ -60,7 +60,6 @@ SKIP: {
@params = ('quiet' => 1,
'-outfile_name' => $outfile,
'diags' => 1,
'stable' => 1,
'maxmb' => 50,
'maxhours' => 1,
'maxiters' => 20,
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