Hello Michael,
by all means, /usr/local/share/cwl sounds like right, too, just let me attemt to quickly serialise all the input my mind gives me:
* In my perception these CWL instructions are mostly independent of the installed software. As such I do not feel the urge to connect those too much with the installation directory of any particular software
* CWL by itself is in /usr/share but that directory is not meant to be touched by anyone/anything. Extra bits that the
end users changes or configures should be in /etc/appname.conf or /etc/appname.d/*
* /usr/local is not used much, with the exception of locally compiled/installed software that is not packaged.
scenario: that locally installed package is CWL-aware, then yes, /usr/local/share/cwl sounds like right
scenario: that locally installed package has never heard of the CWL and the system administrator aims at adding respective instructions, then I would still prefer /etc/cwl.d but am happy to be corrected if that is unappropriate for some reason
* scenario: average Joe Linux user aims at integrating a command line application that ships with his distro and is already installed on the machine he is working with
- that application will be installed in /usr/{bin,lib,share}
- any extra config should not go in /usr/local and not into anything below /usr but /etc/cwl.d
Have you discussed man pages for the individual workflow descriptions?
Best,
Steffen
Gesendet: Dienstag, 07. Juli 2015 um 18:07 Uhr
Von: "Michael Crusoe" <michael.crusoe@gmail.com>
An: "Debian Med Project List" <debian-med@lists.debian.org>
Cc: "Debian Science List" <debian-science@lists.debian.org>
Betreff: Re: Re: Location for CWL tool descriptions
Hello Steffen,
Thank you for your support. I would recommend that local users can use /usr/local/share/cwl for site-wide non-Debian installed software and ${XDG_DATA_HOME}/cwl/${binary-name}.cwl for per-user installed apps.
Hello,
I am happy to see this. I tend to agree that /usr/share/cwl sounds like the right place for everything coming through upstream.
To accomodate for local user (or Debian package maintainer) additions, I suggest to also allow for /etc/cwl.d/ . Some
/etc/cwl.conf may have an option to support any additional set of folders.
Best,
Steffen
> Gesendet: Sonntag, 05. Juli 2015 um 19:03 Uhr
> Von: "Andreas Tille" <andreas@an3as.eu>
> An: debian-med@lists.debian.org, "Debian Science List" <debian-science@lists.debian.org>
> Betreff: Re: Location for CWL tool descriptions
>
> Hi,
>
> I think Michael's proposal is sensible but I think Debian Science
> should be informed as well - so forwarding to this list.
>
> Kind regards
>
> Andreas.
>
> On Sun, Jul 05, 2015 at 03:34:34PM +0000, Michael Crusoe wrote:
> > Hello Debian Med team,
> >
> > The Common Workflow Language [CWL] working group has created a portable
> > method to describe the command line interface of non-interactive
> > (scientific) computing tools.
> >
> > Ideally tool authors would write and ship such descriptions with their
> > tools. In suggesting that they do so we need to provide advice as to where
> > to install said files.
> >
> > I propose that such descriptors be installed into
> > /usr/share/cwl/${binary-name}.cwl
> >
> > For applications not installed site-wide I propose that all CWL tool
> > descriptions should go to $XDG_DATA_HOME/cwl/${binary-name}.cwl
> > $XDF_DATA_HOME is from the XDG Base Directory Specification [XDGBDS]; as
> > per that standard it should be interpreted as $HOME/.local/share if not
> > defined.
> >
> > What do people think? By my reading this is compliant with the Debian
> > Policy Manual but I am happy to hear other suggestions or corrections.
> >
> > [CWL] http://common-workflow-language.github.io
> > [XDGBDS] http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html
> >
> > Cheers,
> >
> > --
> > Michael R. Crusoe
> > --
> > Michael R. Crusoe: Programmer & Bioinformatician crusoe@ucdavis.edu
> > The lab for Data Intensive Biology; University of California, Davis
> > https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
>
> --
> http://fam-tille.de
>
>
> --
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