[Bioperl-l] standardize shebang line in bioperl scripts

Fields, Christopher J cjfields at illinois.edu
Mon Sep 3 22:21:52 UTC 2018

Hi Carnë,

I’d go ahead and implement your plan.  My suspicion is that this will affect very few users.


On August 29, 2018 at 7:12:51 AM, cjfields at illinois.edu (cjfields at illinois.edu<mailto:cjfields at illinois.edu>) wrote:

Yes, pretty inconsistent.  If this is for installation purposes and is bundled with a specific version of perl along with it’s installed dependencies, I would say switch to the perl used for installation.

Personally, I use '#!/usr/bin/env perl’ for most cases, though this is because I work primarily in a cluster environment where the version of perl may change depending on what is loaded into the path at any point.  However this is also primarily for development, not for a typical user.


On August 29, 2018 at 6:36:42 AM, Carnë Draug (carandraug+dev at gmail.com<mailto:carandraug+dev at gmail.com>) wrote:


I was wondering if there's any consensus about what should be used in
the shebang line. Looking at the existing scripts, I found:

#!/usr/bin/env perl
#!/usr/bin/perl -w

Using the bioperl distzilla plugin bundle, 'perl' and '/usr/bin/perl'
get converted to the path of perl used for the package installation.
However, if '/usr/bin/env perl' it remains unmodified. This behaviour
seems to be a bug in MakeMaker [1].

To me it makes sense to have the shebang line replaced with the perl
used for installation since that's the one that will have the rest of
bioperl modules. But the most important thing, I think, is to be

If no one opposes soon, I will change all of them to '/usr/bin/perl'
so that it gets fixed during install.

I will also replace the '-w' flag with the warnings pragma.


[1] https://github.com/Perl-Toolchain-Gang/ExtUtils-MakeMaker/issues/58

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