[med-svn] [Git][med-team/bioperl-run][master] Change kalign command string to input via stdin

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / bioperl-run


Commits:
1d0816c1 by Pranav Ballaney at 2020-03-30T16:38:24+05:30
Change kalign command string to input via stdin
It fails to take input via the -in flag during testing

- - - - -


1 changed file:

- lib/Bio/Tools/Run/Alignment/Kalign.pm


Changes:

=====================================
lib/Bio/Tools/Run/Alignment/Kalign.pm
=====================================
@@ -339,7 +339,7 @@ sub align {
 
 sub _run {
     my ($self,$infilename,$params) = @_;
-    my $commandstring = $self->executable." -in $infilename $params";
+    my $commandstring = "cat $infilename | ".$self->executable." $params";
     
     $self->debug( "kalign command = $commandstring \n");
 



View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/1d0816c1e6114efaa1af54d1f79568a410ad9a8a

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View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/1d0816c1e6114efaa1af54d1f79568a410ad9a8a
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