Hi Steffen,
On Sat, Nov 14, 2020 at 08:18:48PM +0100, Steffen Möller wrote:
> > We have the workaround
> >
> > /usr/lib/debian-med/bin/
> >
> > see for instance in eigensoft[1] and lots of other packages. Simply
> > provide this for picard-tools and make sure gatk users set the PATH
> > accordingly.
>
> Ah - that is good. Seems like I should read our policy document again.
Not sure whether it is mentioned in policy. I introduced this 2 or 3
sprints ago. Finally you are Uploader of at least one package using
this technique. ;-P
> I just checked what my installation has in this directory ... and it
> seems like I spotted a typo (or a creative fix of a typo elsewhere)
?
> $ ls -l /usr/lib/debian-med/bin/
> total 0
> lrwxrwxrwx 1 root root 26 Nov 12 16:57 tranlate ->
> ../../../bin/fsa-translate
>
> $ apt-file search tranlate
> fsa: /usr/lib/debian-med/bin/tranlate
> $ apt-file search /usr/bin/translate
> drslib: /usr/bin/translate_cmip3
> openafs-client: /usr/bin/translate_et
> translate: /usr/bin/translate
>
> I presume you would be happy for me to put there a link from cnvkit.py
> (like bcbio expects it) to /usr/bin/cnvkit, right?
Well, I think its orthogonal to my own happyness. If it works for
you just do the same as in the given example package.
> > Simply ping the authors about this. As far as I remember the last
> > status was that sources are lost (?????) and a backup needs to be found.
>
> And if we just go for a non-free binary package for those jars? Just to
> get somewhere?
I personally consider maintaining non-free packages a pure nuisance and
I'm not motivated to maintain such a package. I think we should do
*way* more effort to free *all* our non-free packages.
> bcbio is in contrib anyway because of vienna-rna.
Same here. I do not see any record of attempts to free vienna-rna.
> And I do not think
> these .jar files
> will find much future adoption without a source backing, so this problem
> will eradicate
> itself.
I will not try to stop anybody to maintain non-free packages - just do
not trust on me in doing so.
> There is also
> bcbio.pipeline.config_utils.CmdNotFound: '_get_program_cmd' 'snpEff'
> {'dir': '/usr/local/share/java/snpeff', 'jvm_opts': ['-Xms750m',
> '-Xmx3g']} None
I think we are pretty close to snpEff due to Pierre's efforts.
> ... picard-tools stuff snipped - I have nothing to say here ...
> Somehow Debian does barely complete any of these tests. There is always
> something missing. And if it is tophat that upstream had asked us not to
> support any more.
I asked *several* times whether we need tophat and consequently will do
a Python3 port. Its perfectly fine for me to re-introduce tophat once
it works with Python3.
Kind regards
Andreas.
--
http://fam-tille.de
