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Hi Ben,
That's an interesting find. Alke's filter-stage-1.prl script should be better at reporting when it cannot find a dependent program. I added the following code to the script:
use File::Which;
unless ( which( $TRF_COMMAND ) && which( $NSEG_COMMAND ) )
{
die "ERROR: RepeatScout script filter-stage-1.prl cannot find 'trf' or 'nseg' programs in the user's path!\n";
}
This should at least produce an error message that will indicate something went wrong. I don't see why you would need to get rid of the "$ENV{'TRF_COMMAND'} ||" portion as that is simply a conditional statement which allows you to have environmental variables set to point to the programs location. Perhaps you have these environmental variables set and set incorrectly? Perhaps when you ran the program you hadn't updated the shell's path in memory ( using rehash command )? In any case, I am glad you got it working. I will push this change to filter-stage-1.prl out in the next release of RepeatScout.
That's an interesting find. Alke's filter-stage-1.prl script should be better at reporting when it cannot find a dependent program. I added the following code to the script:
use File::Which;
unless ( which( $TRF_COMMAND ) && which( $NSEG_COMMAND ) )
{
die "ERROR: RepeatScout script filter-stage-1.prl cannot find 'trf' or 'nseg' programs in the user's path!\n";
}
This should at least produce an error message that will indicate something went wrong. I don't see why you would need to get rid of the "$ENV{'TRF_COMMAND'} ||" portion as that is simply a conditional statement which allows you to have environmental variables set to point to the programs location. Perhaps you have these environmental variables set and set incorrectly? Perhaps when you ran the program you hadn't updated the shell's path in memory ( using rehash command )? In any case, I am glad you got it working. I will push this change to filter-stage-1.prl out in the next release of RepeatScout.
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