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

[Andreas Tille]

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