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tseemann / VelvetOptimiser

:chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters.
GNU General Public License v2.0
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Problem with perl's rename #22

Closed EugeneBragin closed 6 years ago

EugeneBragin commented 6 years ago

In certain circumstances perl's rename would fail quietly. https://github.com/tseemann/VelvetOptimiser/blob/master/VelvetOptimiser.pl#L404 This happens for example when using velvetoptimiser in a docker container when -d is set to another volume. Tracing the error gives following: bash-4.2# perl -e "rename('/auto_data_83','/data/assembly') or die \$!;" Invalid cross-device link at -e line 1. Would be great have the exception handled with or die ...$! and/or perhaps consider using mv?

P.S. https://www.unix.com/shell-programming-and-scripting/27747-perl-rename-failed.html

Slugger70 commented 6 years ago

Thanks Eugene. I'll look into it.

Slugger70 commented 6 years ago

Fixed in PR #23