Re: Initial Grinder package
Charles Plessy-12 wrote: Florent, since the files in /inc are also distributed as Debian packages: are they strictly neeeded, or could they be omitted? That would reduce the code duplication in our archive. Thanks for the help with the package upload, Charles. What you ask is a good question. I think this is possible but it is sort of going against the philosophy of Module::Install To achive what you suggest requires adding libmodule-install-perl (and other modules that have files in inc) as a build-dependency of the package. Then the files under inc/ but not the inc/ directory itself need to be deleted, otherwise Module::Install will think it is being called by the author of the module instead of a user (see http://search.cpan.org/~adamk/Module-Install/lib/Module/Install/Admin.pm#Bootstrapping). Changing the first line of the Makefile.PL from 'use inc::Module::Install;' (to use the modules in inc/) to 'use inc::Module::Install;' (to use their system-wide quivalent) is not an option since it generates an error. The perl-pkg group does not seem to strip inc/ for their packages that use Module::Install. Maybe it is not worth the trouble. Florent -- View this message in context: http://old.nabble.com/Initial-Grinder-package-tp33185950p33234029.html Sent from the debian-med mailing list archive at Nabble.com. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/33234029.p...@talk.nabble.com
Re: Initial Grinder package
Hi Andreas, Thank you for your advices. The only thing I would like you to change is the authorship of the manpages. While it is correct that you can claim yourself as the author of the manpage it would be more precise to inform that you did this by the help of help2man for the Debian distribution and upstream is free to take over these. (There is some kind of fixed phrase for Debian written manpages which you can look up in our SVN repository in several examples or at other places.) If you have done so feel free to ping me again for an upload. I could not find the fixed phrase you mention. However, I noticed that packages which rely on help2man like Velvet or Bowtie omit the [author] section in their manpages. I am now following their example for the Grinder package. I believe that this should address your issue. I also added a basic load test. Does one generally need to ping you for every upload, or is it generally sufficient to modify the changelog file from 'UNRELEASED' to 'unstable'? Best, Florent -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4f222b63.1090...@gmail.com
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Introduction
Dear DebianMed list, I just joined the group. I am a computational biologist, a microbial ecologist specifically, who uses mostly Perl when coding. I have been using Debian-based Linux distros for quite some time (Linux Mint Debian Edition at the moment) and became interested in packaging software for Debian. I maintain a few Perl modules on CPAN (http://search.cpan.org/~fangly/ http://search.cpan.org/%7Efangly/) and have recently uploaded my first deb package, Math::Random::MT::Perl, at http://mentors.debian.net/package/libmath-random-mt-perl-perl. I have also joined the Debian Perl group. DebianMed has already packaged great programs that are useful to microbial ecologists (e.g. QIIME, Velvet). There are other ones that could be useful and that I could try to package. For example, MetaVelvet is an assembler specific to metagenomic datasets (but I do not know if is mature enough for packaging yet). Another example is Grinder (http://sourceforge.net/projects/biogrinder/) software to simulate amplicon and shotgun datasets. Thanks for letting me join the group and best regards, Florent
