[Debian-med-packaging] r17340 - trunk/packages/velvet/trunk/debian

[Andreas Tille]

As you might have noticed by recent commits I noticed where
VelvetOptimiser is packaged and you can skip this part of my mail.

On Mon, Jun 30, 2014 at 11:47:53AM +0200, Andreas Tille wrote:
> Hi Tim,
> 
> thanks for propagating useful changes to the Debian packages of velvet.
> Before I upload your changes I would like to make sure that I have
> understood everything correctly.  So I'm adding some questions to your
> changes below:
> 
> On Mon, Jun 30, 2014 at 08:53:16AM +0000, Timothy Booth wrote:
> > Author: tbooth-guest
> > Date: 2014-06-30 08:53:16 +0000 (Mon, 30 Jun 2014)
> > New Revision: 17340
> > Added:
> >    trunk/packages/velvet/trunk/debian/VelvetOptimiser.README
> >    trunk/packages/velvet/trunk/debian/velvet-long.install
> > Modified:
> >    trunk/packages/velvet/trunk/debian/changelog
> >    trunk/packages/velvet/trunk/debian/control
> >    trunk/packages/velvet/trunk/debian/rules
> >    trunk/packages/velvet/trunk/debian/velvet.install
> > Log:
> > Sync package with Bio-Linux version.  If the changes are accepted as-is, then
> > VelvetOptimiser should be added to Debian.
> 
> What do you mean by "VelvetOptimiser should be added to Debian"?  Do you
> have some separate packaging?  I vaguely remember that we discussed this
> previously (to lazy to seek the archive - seems you have better
> information anyway).  If you have some packaging it would be great if
> you could inject this as well into VCS and I'll upload to new.
>  
> > ...
> > Modified: trunk/packages/velvet/trunk/debian/rules
> > ===================================================================
> > --- trunk/packages/velvet/trunk/debian/rules	2014-06-30 08:36:48 UTC (rev 17339)
> > +++ trunk/packages/velvet/trunk/debian/rules	2014-06-30 08:53:16 UTC (rev 17340)
> > @@ -9,34 +9,61 @@
> >  pkg=velvet
> >  
> >  override_dh_auto_clean :
> > +	# If tarball was not pre-cleaned this will do it.
> >  	dh_auto_clean
> >  	rm -rf zlib
> > +	rm -rf third-party
> > +	rm -rf debian.upstream
> > +	rm -f *.pdf
> 
> Any reason to kick the *.pdf files from the source archive?
> 
> > +	find -name '._*' -delete
> 
> These files should not be in the uploaded source tarball anyway.  I'd
> recommend just sticking to the source tarball in the Debian archive for
> md5sum identical source tarballs.
> 
> > +	rm -rf data.tar.*
> >  
> > -override_dh_auto_build :
> > +build_long_versions :
> > +	touch zlib
> > +	#Make _long version
> > +	dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
> > +	mv velveth velveth_long ; mv velvetg velvetg_long
> > +	#Make _63 kmer version
> > +	dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
> > +	mv velveth velveth_63 ; mv velvetg velvetg_63
> > +	#And also one with both options
> > +	dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
> > +	mv velveth velveth_63_long ; mv velvetg velvetg_63_long
> > +
> > +override_dh_auto_build : build_long_versions
> >  	touch zlib # prevents the zlib in the ‘third-party’ folder to be built.
> >  	dh_auto_build -- OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
> >  	dh_auto_build -- color OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
> > +	#Pack the examples
> > +	tar -cvaf data.tar.xz data
> 
> Could you please explain the role of this data.tar.xz?
> 
> >  override_dh_install :
> > -	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
> > +	mkdir -p debian/$(pkg)/usr/share/man/man1/
> >  	help2man --no-info --name="simple hashing program" \
> > -	         $(CURDIR)/velveth > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1
> > +	         ./velveth > debian/$(pkg)/usr/share/man/man1/velveth.1
> >  	help2man --no-info --name="simple hashing program (colorspace version)" \
> > -	         $(CURDIR)/velveth_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth_de.1
> > +	         ./velveth_de > debian/$(pkg)/usr/share/man/man1/velveth_de.1
> >  	help2man --no-info --version-option=" " \
> >  	         --name="de Bruijn graph construction, error removal and repeat resolution" \
> > -	         $(CURDIR)/velvetg > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg.1
> > +	         ./velvetg > debian/$(pkg)/usr/share/man/man1/velvetg.1
> >  	help2man --no-info --version-option=" " \
> >  	         --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \
> > -	         $(CURDIR)/velvetg_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg_de.1
> > +	         ./velvetg_de > debian/$(pkg)/usr/share/man/man1/velvetg_de.1
> >  	dh_install
> > -	rm -rf $(CURDIR)/debian/$(pkg)/usr/share/velvet/contrib/MetaVelvet-v0.3.1/obj
> >  	# remove extra copies of GPL
> >  	find $(CURDIR)/debian -type f -name 'LICENSE*' -delete
> > +	#MetaVelvet should be scrubbed, and VelvetOptimiser is now separate.  Note that these
> > +	#will not have been installed if this was a binarry-only build.
> > +	[ ! -e debian/velvet-example/usr ] || \
> > +	  rm -r debian/velvet-example/usr/share/doc/velvet/contrib/MetaVelvet*
> 
> May be it is sensible to drop MetaVelvet from the source tarball at all
> and add it to Files-Excluded.  What do you think?
> 
> > +	[ ! -e debian/velvet-example/usr ] || { \
> > +	  rm -r debian/velvet-example/usr/share/doc/velvet/contrib/VelvetOptimiser* && \
> > +	  cp debian/VelvetOptimiser.README debian/velvet-example/usr/share/doc/velvet/contrib/ \
> > +	; }
> 
> To rephrase my question from the beginning:  Where will this separate
> VelvetOptimiser be?
> 
> Thanks for your work on this package
> 
>     Andreas.
> 
> -- 
> http://fam-tille.de
> 
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