Re: cloud image preparation - kind of there
Hello,
On 08/08/2010 04:16 PM, Charles Plessy wrote:
> 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.
>
> 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.
Charles, this is excellent. Andreas, if you don't veto this, then let us
please start with such a manual setup and then find ways to autogenerate
that from whatever source this may be. debtags come to mind, indeed. We
would not even need a change in apt to get this implemented.
Below changes (very little) and a full version attached. I moved *bagphenotye*
to "suggests" since the package is not yet uploaded, and garlic is gui-driven.
Another immediate question is to what degree the image should be mostly of
those bioinformatics packages. I could well imagine to have some more diversity
or many different images for the various tasks of ours available.
I'll upload our current version (a superset of this med-cloud), 2GB worth,
tonight to spawn some more discussions.
Best,
Steffen
--- cloud.charles 2010-08-08 17:45:26.000000000 +0200
+++ cloud.steffen 2010-08-08 17:50:50.000000000 +0200
@@ -16,11 +16,13 @@
X-Begin-Category: Genetics
Depends:
alien-hunter,
- bagphenotype,
loki,
plink,
r-cran-qtl,
- r-other-mott-happyfastlink,
+ r-other-mott-happy,
+ fastlink
+Suggests:
+ bagphenotype,
r-other-valdar-bagphenotype.library
X-End-Category: Genetics
@@ -82,7 +84,6 @@
X-Begin-Category: Molecular modelling and molecular dynamics
Depends:
- garlic,
gromacs,
mustang,
theseus
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,
loki,
plink,
r-cran-qtl,
r-other-mott-happy,
fastlink
Suggests:
bagphenotype,
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:
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.
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