AW: Question regarding ResFinder

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AW: Question regarding ResFinder

Andreas Tille
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:[hidden email]]
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" <[hidden email]> 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:[hidden email]]
    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
    [hidden email]
    http://www.dtu.dk/english
   
   
   
    On 11/06/2018, 12.25, "Banerji, Sangeeta" <[hidden email]> 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
       
   
   

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Re: Question regarding ResFinder

Andreas Tille-6
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:[hidden email]]
> 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" <[hidden email]> 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:[hidden email]]
>     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
>     [hidden email]
>     http://www.dtu.dk/english
>    
>    
>    
>     On 11/06/2018, 12.25, "Banerji, Sangeeta" <[hidden email]> 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