Re: cloud image preparation - kind of there

[Charles Plessy <plessy@debian.org>]

Le Sun, Aug 08, 2010 at 09:21:35AM +0200, Andreas Tille a écrit :
> 
> Now I understand the motivation for a med-bio-console (I continue to
> think that headless is a suboptimal word) a bit better.  However I'm not
> very comfortable with separating packages only because of their user
> interface.  Here rather comes another potential use case of DebTags into
> mind.  I have not yet a suggestion for an immediately applicable
> solution but IMHO we should think into this direction.

Hi Andreas,

I also think that there is no immediate solution that is completely satisfying.
As soon as an apt front-end will support Debtags, the split will lose its
interest, but I do not even know if somebody is working on this. Making med-bio
depend on med-bio-headless would depend on your effort to implement
Meta-Depends if we want to keep nice task pages.

In the end, it seems that we need a short-term solution. As suggested on
http://wiki.debian.org/DebianScience/ProblemsToWorkOn#Morefinegrainedtasks, how
about a new task, for instance “med-cloud”? Here is a suggested tasks file. Let
me know if you would like me to commit it. For the moment it is only a subsed
of med-bio, but it would make sense to add other command line programs that do
not depend on graphical toolkits.

Cheers,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan

Task: Cloud
Description: Cloud computing image for Debian Med.
 This metapackage will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences, that do not
 depend on graphical toolkits and therefore can fit on system images for use
 in cloud computing clusters, where space can be limited.

X-Begin-Category: Phylogenetic analysis
Depends:
	altree,
	fastdnaml,
	phyml,
	tree-puzzle | tree-ppuzzle
X-End-Category: Phylogenetic analysis

X-Begin-Category: Genetics
Depends:
	alien-hunter,
	bagphenotype,
	loki,
	plink,
	r-cran-qtl,
	r-other-mott-happyfastlink,
	r-other-valdar-bagphenotype.library
X-End-Category: Genetics

X-Begin-Category: Sequence alignments and related programs.
Depends: 
	amap-align,
	blast2
	boxshade,
	dialign,
	dialign-tx,
	exonerate,
	gff2aplot,
	glam2,
	gmap,
	hmmer,
	kalign,
	mafft,
	mummer,
	muscle,
	poa,
	probcons,
	proda,
	python-pynast,
	sibsim4,
	sigma-align,
	sim4,
	t-coffee,
	wise
Depends:     clustalw | clustalw-mpi
Comment: non-free
X-End-Category: Sequence alignments and related programs.

X-Begin-Category: EMBOSS
Depends:
	emboss,
	embassy-domalign,
	embassy-domainatrix,
	embassy-domsearch,
	embassy-phylip
X-End-Category: EMBOSS

X-Begin-Category: High throughput sequencing
Depends:
	bwa,
	last-align,
	maq,
	picard-tools,
	r-bioc-hilbertvis,
	samtools,
	ssake,
	velvet
X-End-Category: High throughput sequencing

X-Begin-Category: Analysis of RNA sequences.
Depends:
	infernal,
	rnahybrid
X-End-Category: Analysis of RNA sequences.

X-Begin-Category: Molecular modelling and molecular dynamics
Depends:
	garlic,
	gromacs,
	mustang,
	theseus
Depends: autodock, raster3d
Comment: non-free
X-End-Category: Molecular modelling and molecular dynamics

X-Begin-Category: Tools for the molecular biologist.
Depends:
	acedb-other,
	melting, mipe,
	ncbi-epcr,
	ncbi-tools-bin,
	ncoils,
	primer3,
	readseq,
	tigr-glimmer,
	seqan-apps,
	staden-io-libs-utils
Depends: python-cogent
Comment: non-free
X-End-Category: Tools for the molecular biologist.