[Bioperl-l] bioperl executables files and dist-zilla

[Carnë Draug]

On 9 January 2015 at 18:33, Fields, Christopher J <cjfields at illinois.edu> wrote:
> On Jan 9, 2015, at 11:57 AM, Carnë Draug <carandraug+dev at gmail.com> wrote:
>>
>>
>> So I'm proposing that as we move modules from bioperl-live into the smaller
>> distributions, we also move them to a "bin/" directory as part of the
>> configuration for dzil (no symlinking required).
>> [...]
>>
>
> Yep, agreed (see above).

Seems like I already knew this before since I fixed that for Bio-Biblio
almost 2 years ago [1].

I have just changed this on Bio-FeatureIO, Bio-SearchIO-Writer-BSMLResultWriter,
and Bio-Community.

>>> Re: extensions, I wouldn’t have a problem with this except that old
>>> installations of the scripts would still be around, correct? If so, we
>>> would need to add a bit of code that checks for the presence of old
>>> versions and removes/replaces them.  Might be more trouble than it’s worth.
>>
>> Isn't the file extension removed during installation of bioperl?
>> I remember that the "bp_" was added automatically, a step which we
>> dropped in favour of simply having the files already with the "bp_".
>> I thought that it was the same with the file extension.
>>
>> Carnë
>>
>> [1] https://github.com/bioperl/Bio-EUtilities/commits/master
>
> On our local cluster installation (we have a few default installations
> packaged up for various tools) the ‘.pl’ is still present.  For example, in
> our standard base local perl installation (5.16 at the moment):
>
> -system-specific-4.1$ module load perl
> -system-specific-4.1$ bp_
> bp_aacomp.pl                  bp_fetch.pl                   bp_mutate.pl                  bp_search2table.pl
> bp_biblio.pl                  bp_filter_search.pl           bp_netinstall.pl              bp_search2tribe.pl
> [...]

You are right. I only install bioperl-live from the repositories (Debian), so
I never noticed that it was Debian's doing.  Checking Debian's diff [2], I now
see:

    +    # prename is the rename utility written in perl usually
available as /usr/bin/rename in Debian.
    +    prename s/.pl$$// debian/bioperl/usr/bin/*pl
    +    prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p

Why the extension once installed? That seems very uncommon.  Just running
`grep -lP '^#!.*perl' /usr/bin/*` shows several but none have a file
extension. Same for python and sh, the executables do not typically keep
the file extension of the language they are written on.

Carnë

[1] https://github.com/bioperl/Bio-Biblio/commit/cbe34d52696d9157d71c853ef96849d455fcc780
[2] http://ftp.de.debian.org/debian/pool/main/b/bioperl/bioperl_1.6.1-2.diff.gz