Re: packaging UCSC kent tools for debian-med
Hi Hiram,
thanks for your quick response. May be I stressed the wrong fact since
the main point was the license of the sources inside the tarball which
was previously discussed here:
http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-March/025520.html
Debian can not distribute this code.
Kind regards
Andreas.
On Sun, Oct 18, 2015 at 05:43:30AM -0700, Hiram Clawson wrote:
> Good Morning Andreas:
>
> Yes, the versioned tar balls can be seen here:
>
> http://hgdownload.cse.ucsc.edu/admin/exe/
>
> Note the userApps.vNNN.src.tgz files
> with the newest one always as simply userApps.src.tgz
>
> These binaries can be built thusly:
>
> rm -fr userApps
> wget --timestamping http://hgdownload.cse.ucsc.edu/admin/exe/userApps.src.tgz
> tar xvzf userApps.src.tgz
> cd userApps
> MAKE="make -j 24" make -j 24 > make.log 2>&1
>
> Resulting binaries end up in userApps/bin/
>
> The versioned tarballs do not unpack into unique named directories,
> they unpack in the same 'userApps' binary:
>
> This is the same result:
>
> rm -fr userApps
> wget --timestamping http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v323.src.tgz
> tar xvzf userApps.v323.src.tgz
> cd userApps
> MAKE="make -j 24" make -j 24 > make.log 2>&1
>
> Please note the userApps/README file for expected system requirements
> and alternative build procedures using 'git', for example:
>
> http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README
>
> This code will not compile nor function on sparc or alpha machines.
> Only x86_64 and Mac OSX have been tested. There is no comprehensive test suite,
> although some binaries do have a 'make test' target but it is all a manual
> procedure, nothing automatic.
>
> --Hiram
>
> On 10/18/15 12:12 AM, Andreas Tille wrote:
> >Hi,
> >
> >are there any news about versioned tarballs of your software at
> >genome-source.cse.ucsc.edu ?
> >
> >Kind regards
> >
> > Andreas.
> >
> >On Wed, Aug 27, 2014 at 11:04:13AM +0200, Andreas Tille wrote:
> >>Hi again,
> >>
> >>please see my additions inline!
> >>
> >>
> >>On Wed, Aug 27, 2014 at 10:52:35AM +0200, Andreas Tille wrote:
> >>>Hi Hiram,
> >>>
> >>>I hope you don't mind if I'm putting Debian Med list in the discussion
> >>>which I would like you to do in pure technical discussion as well.
> >>>
> >>>On Wed, Aug 27, 2014 at 12:00:59AM -0700, Hiram Clawson wrote:
> >>>>Good Evening Andreas:
> >>>>
> >>>>I'm curious if there would be a way to fit this building procedure
> >>>>into the Debian-Med project:
> >>>>
> >>>> http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README
> >>>>
> >>>>Note steps 1, 2, 3 near the top of the README after the 'System Requirements'
> >>>>discussion.
> >>>>
> >>>>I fully realize this isn't they way packages are supposed to work, but at
> >>>>this time, this is the best we have.
> >>>
> >>>Simply from reading the README I can not see anything unusual. Step 1
> >>>(fetching the tarball) is totally normal workflow,
> >>
> >>Some correction to what I said here: Please provide a *versioned*
> >>tarball! Every tarball should have a version to be able to detect updates.
> >>
> >>Moreover once I have checked the tarball I realised that the problematic
> >>license which was discussed previously[0] remains. So *if* this software
> >>should be distributed by Debian this needs to be fixed first.
> >>
> >>>step 2 is cd-ing to
> >>>the unpackaged dir and call make is also pretty normal except that this
> >>>make call is done by the debhelper tools. The only difference is step 3
> >>>where we do not move files to /usr/local but rather into /usr/bin inside
> >>>the Debian package.
> >>>
> >>>>Perhaps there could be a way to
> >>>>encapsulate these first three steps into some kind of building/packaging
> >>>>business that would satisfy the standard build and packaging procedures ?
> >>>
> >>>Yes, for sure. That's the day job of a Debian packager. Do you want to
> >>>learn how to do this? If yes we could offer mentoring in the so called
> >>>Mentoring of the Month[1] effort. While there is right now the
> >>>September slot occupied I would try hard to help you as well since if we
> >>>want to get these tools included (and I would really love to see this)
> >>>we need to start right now.
> >>>
> >>>So are you able to invest some time slots into the packaging and want to
> >>>work together with us please subscribe this mailing lists (links should be
> >>>given on the Wiki page[1]) and ask for help here in case of trouble or
> >>>if you need some kickstart help.
> >>>
> >>>Thanks for your interest in Debian Med
> >>>
> >>> Andreas.
> >>>
> >>>[1] https://wiki.debian.org/DebianMed/MoM
> >>
> >>[0] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-March/025520.html
> >>
> >>--
> >>http://fam-tille.de
> >>
> >>
> >>--
> >>To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
> >>with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
> >>Archive: https://lists.debian.org/20140827090413.GC25601@an3as.eu
> >>
> >>
> >
>
--
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