Hi again,
I've checked resfinder again. It is now at version 3.1 and the download
archive contains:
1. resfinder.pl - the program
2. resfinder.py - (same program using an available blastn version -
blastn-2.2.26+)
I admit I have no idea what program should be exposed to the user in the
system PATH.
Kind regards
Andreas.
On Mon, Jun 25, 2018 at 02:26:00PM +0000, Tille, Andreas wrote:
> Dear Rolf,
>
> thanks a lot for the clarification. I've adapted the preliminary Debian
> packaging to this tag.
>
> Unfortunately I have some further issues:
>
> 1. There is some missing Perl module:
>
> $ resfinder.pl
> Can't locate Try/Tiny/Retry.pm in @INC (you may need to install the
> Try::Tiny::Retry module) (@INC contains: /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.26.2 /usr/local/share/perl/5.26.2
> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5
> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
> /usr/bin/resfinder.pl line 9.
> BEGIN failed--compilation aborted at /usr/bin/resfinder.pl line 9.
>
> There exists some Debian packaged Retry.pm:
> libfile-flock-retry-perl: /usr/share/perl5/File/Flock/Retry.pm
> No idea whether this will work as well. Or do we need this one
> https://metacpan.org/pod/Try::Tiny::Retry ?
>
> 2. You will probably not like to change the file name
> but there is some good advise to not add the programming
> language of some program to the file name.
>
> https://wiki.debian.org/UpstreamGuide#Language_extensions_in_scripts
> One of the reasons given there is very true for your current
> situation where the code is rewritten - at some point in time
> there will be resfinder.py and your users need to learn some new
> name while they most probably do not care at all about programming
> languages. I'd recommend to at least not use the *.py extension
> in future versions.
>
> 3. In INSTALL_DB you hard code non-annonymous cloning from a git
> repository. I've added a patch
>
> https://salsa.debian.org/med-team/resfinder/blob/master/debian/patches/anonymous_cloning_db.patch
> to enable any user cloning the database.
>
> Kind regards
>
> Andreas.
>
> -----Ursprüngliche Nachricht-----
> Von: Rolf Sommer Kaas [mailto:[email protected]]
> Gesendet: Dienstag, 19. Juni 2018 11:36
> An: Tille, Andreas; Banerji, Sangeeta
> Betreff: Re: Question regarding ResFinder
>
> Dear Andreas,
>
> I finally got around to look into this. It was a little complicated, as the
> version number didn’t match what I expected, and I have not been responsible
> for previous versions of ResFinder, so I had to make sure which version was
> currently on the master branch. It turned out that the version number in the
> code was incorrect. It is actually version 2.3 that is on the master branch.
> I’ve corrected the code and created the appropriate tag.
>
> When we release version 4, we will have done a lot of cleaning up and the
> releases, branches and so on will hopefully be following the standards of
> GitFlow.
>
> Best,
> Rolf
>
>
>
> On 15/06/2018, 08.26, "Tille, Andreas" <[email protected]> wrote:
>
> Dear Rolf,
>
> thanks for the clarification. From the line
>
> use constant VERSION => '2.1';
>
> in file resfinder.pl I assumed that the Perl version of ResFinder is
> version 2.1 and from your mail that is the stable version. Could you please
> enable downloading a tar.gz archive of this stable version. While I'm
> perfectly able to clone the Git repository it is not fully clear whether
> "random" Git commits that might go beyond a version 2.1 "release" are just
> development code that is leading to a possible new release 2.2 of the Perl
> code or whether users are supposed to install the latest Git commit. As
> Sangeeta wrote my intention is to package all software we are using for
> official Debian and there we have tools checking for new version according to
> downloadable tarballs. The release of a tarball is a signal what software
> developers want users to be installed on their machines.
> Unfortunately I have no idea how the tarball creation works on bitbucket.
> On Gitlab and Github it is just by creating a release tag. I assume it will
> be equally simple on bitbucket (a quick search uncovered
> https://confluence.atlassian.com/bitbucket/use-repository-tags-321860179.html
> which seems to support my assumption).
>
> Kind regards and thanks for your cooperation
>
> Andreas.
>
> -----Ursprüngliche Nachricht-----
> Von: Rolf Sommer Kaas [mailto:[email protected]]
> Gesendet: Montag, 11. Juni 2018 23:20
> An: Banerji, Sangeeta
> Cc: Tille, Andreas
> Betreff: Re: Question regarding ResFinder
>
> Dear Sangeeta and Andreas,
>
> The branch 4.0 is the development branch for ResFinder 4.0 and is not
> published, and not ready to run outside DTU.
>
> The master branch is the current published/stable version.
>
> We are working very hard on getting 4.0 published as it is a complete
> reimplementation of ResFinder and it adds a mapping based solution along with
> a completely new database, that attempts to translate genotypes to
> phenotypes. If you wish to receive an email when we are ready to beta test
> 4.0, I’ll be happy to put you on the list?
>
> Best regards,
> Rolf Sommer Kaas
> Researcher
> Research Group for Genomic Epidemiology
> National Food Institute
> ------------------------------------
> Technical University of Denmark
> Søltofts Plads
> Building 221, Room 054
> 2800 Kgs. Lyngby
> Direct +45 35886333
> [email protected]
> http://www.dtu.dk/english
>
>
>
> On 11/06/2018, 12.25, "Banerji, Sangeeta" <[email protected]> wrote:
>
> Dear Rolf,
> I have a question regarding ResFinder and I hope you can answer it. I
> asked our linux guy (Andreas Tille) to package ResFinder for Debian. However,
> he wonders why there are two different codes available. A perl code and a
> python code: https://bitbucket.org/genomicepidemiology/resfinder.git and
> https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=branches
>
> Are both codes updated and equal or should we prefer one of them for
> Debian packaging? Also, Andreas could not find a copy of the Apache license
> with the code. I see that you have a link to Apache 2.0 license on the
> ResFinder bitbucket site but maybe you should also distribute it with the
> code.
>
> All the best,
> Sangeeta
>
>
>
>
--
http://fam-tille.de
