-smp use in rf-fold

[Asperatus22]

Hi all, i notice a possible issue in rf-fold: In the help, it is notice that -smp version of RNA structure would be use by default if available, but it does'nt use this -smp version in my config, despite the presence of the two version :

(RNAframework) []$ which ShapeKnots /nfs/conda/envs/RNAframework/bin/ShapeKnots

(RNAframework) []$ which ShapeKnots-smp /nfs/conda/envs/RNAframework/bin/ShapeKnots-smp

when i run rf-fold on my server, it run ShapeKnots

I create a .pl test file with the folowing script : (i'm not aware of Perl langage...)

!/usr/bin/env perl

use strict; use Config; use Cwd; use File::Basename; use File::Which; use File::Path qw(mkpath); use File::Spec; use FindBin qw($Bin); use Getopt::Long qw(:config no_ignore_case); use POSIX qw(floor); use threads; use threads::shared;

use lib $Bin . "/lib";

use constant MINWINLENGTH => 50; # Minimum window length for windowed folding my($shapeknots) ;

$shapeknots = File::Spec->rel2abs($shapeknots || which("ShapeKnots"|| which("ShapeKnots-smp") )); #from line 198 in rf-fold script

print $shapeknots

it return:

/nfs/conda/envs/RNAframework/bin/ShapeKnots

notice that i need to add use File::Which;

if i invert the order of the Which it print ShapeKnot-smp.

it should be the same problem with "Fold", in line 197 and "partition" in line 199

best regards

Lionel

[dincarnato]

Hi Lionel,

thanks for reporting! Indeed, this was changed some time ago for tests and I forgot to change it back. It should be fixed now. Please issue a git pull.

All the best, Danny

[Asperatus22]

Hi Danny i think the problème is back this the correction you made on 31 of jully on rf-fold. thanks for your work Lionel

[dincarnato]

Yes, I'm aware, will release the new RNAFramework later today with that fix included

[dincarnato]

You can git pull v2.8.4