Re: Please choose a free license for eigensoft
Dear Andreas,
Thank you for flagging these issues. We have now released EIGENSOFT
6.1.3 with ploteig restored. We have elected to restore the use of
.perl file names for PERL scripts for backwards compatibility.
Sincerely,
Alkes
On 7/19/16, Andreas Tille <andreas@an3as.eu> wrote:
> Hi,
>
> On Mon, Jul 18, 2016 at 03:06:56PM -0400, Alkes Price wrote:
>> Dear Andreas,
>>
>> We have now released EIGENSOFT 6.1.2 with a new license, per your
>> request.
>
> Thanks a lot for this. While taking care for the packaging I noticed
> that the ploteig executable which smartpca.pl is refering to is missing
> from this release.
>
> When checking the code smartpca.pl is also refering to evec2pca-ped.perl
> as well as evec2pca.perl - but both scripts are not named .perl but
> rather .pl.
>
> I have a general remark to those .pl extensions. According to the
> Debian upstream guide[1] it is not a good idea to add language
> extensions to scripts at all (just read the link[1] to learn several
> good reasons why). Since I try to follow the Debian standards inside
> the packaging I'm moving the real executables that are called by *.pl
> wrappers to /usr/lib/eigensoft and keep only the wrappers inside the
> user PATH (/usr/bin) while stripping the extensions. The wrappers are
> patched to find the files in /usr/lib/eigensoft. To keep the
> functionality of possibly existing user scripts in addition the names
> with *.pl extension are provided inside /usr/lib/debian-med/bin and a
> README is added that will inform users to set their PATH accordingly.
> However, I'd recommend to find a similar solution without those
> extensions for all eigensoft users for the reasons I pointed to above.
>
> Another hint: gc.pl (or just gc) is a very generic name that should
> not be used. In the Debian package I install it as
>
> /usr/bin/gc-eigensoft and
> /usr/lib/debian-med/bin/gc.pl
>
> Please consider a better name since the name gc is just choosen by
> graphviz.
>
> Kind regards and thanks again for your cooperation
>
> Andreas.
>
> [1] https://wiki.debian.org/UpstreamGuide#Language_extensions_in_scripts
>
> --
> http://fam-tille.de
>
--
Dr. Alkes Price, Associate Professor / Associate Member
Harvard T.H. Chan School of Public Health, Depts of Epidemiology and
Biostatistics
Broad Institute of MIT and Harvard, Program in Medical and Population Genetics
Building 2, Room 211, 665 Huntington Ave, Boston, MA 02115
aprice@hsph.harvard.edu, phone: 617-432-2262, fax: 617-432-1722
http://www.hsph.harvard.edu/faculty/alkes-price/
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