I like what I saw about biomaj. What is cannot do for the
moment (from what I understood) is to express a runtime
dependency against a particular database version and have
that then installed package trigger biomaj to perform
that step. Correct me if I am wrong, please. Could that be
added?
What
Hi,
there is the BioMAJ tool, currently in packaging for Debian.
Biomaj takes a property file that describes a remote data bank and the
post-processes to apply on the downloaded data.
You can get more info at http://biomaj.genouest.org.
Biomaj takes in charge the download, the postprocesses and
The web interface will have togo to non-free 'cause it depends on
several GWT libraries which are not packaged for Debian so we need to
provide the Jar files with the softs.
The core e.g. the main program that is called by the web interface
will be in free.
Core can also be used without the
Ok, great. Is the core package working and available in SVN? I will give it
a try.
Scott
On Feb 16, 2011, at 10:58 AM, Olivier Sallou wrote:
The web interface will have togo to non-free 'cause it depends on several GWT
libraries which are not packaged for Debian so we need to provide the
Both are available in SVN but those are not officially validated. My
mentor is analysing it to push it.
I tested those however.
In Alioth, there is a get-orig-source to create source file and create
package.
It also requires a mysql db (it is mentioned in man page)
Olivier
Le 2/16/11 6:00
Hi,
On Wed, Feb 16, 2011 at 06:04:46PM +0100, Olivier Sallou wrote:
Both are available in SVN but those are not officially validated. My
mentor is analysing it to push it.
I tested those however.
In Alioth, there is a get-orig-source to create source file and create
package.
It also
I don't disagree, in principle. There are many nice aspects to the debian
packaging as you indicate. We don't want to replicate the 100s of terabytes of
data into the debian repository, so any package would not have the real data
but would download the data from its source during the package
Data versioning is very difficult as all data sources do not keep old
versions online, only a current one.
With biomaj we propose to keep old versions (or a number of old
versions), but this is locally, it cannot help to reproduce an
experiment with exactly the same data if remote source
Hello,
I wonder if anybody has thought about providing large data sets, like genomes,
microarray data, etc. into debian packages in a way that makes it easy for
users to get those data sets onto their machine, making it easier to use
various tools? I can think of many great ways this would be
Hi Scott,
I think your idea is quite reasonable in principle. As far as I
understood (but I did not dived into this) the getData effort[1] is one
step into this direction and the to be soon uploaded package Biomaj does
something that might be helpful as well.
Regarding to actually buold
just few cents. In the domain of neuroimaging we are also confronted
with the problem of distributing data. Various aspects are relevant to
this question if someone is to package data statically (instead of
fetching via some data-sharing framework) into a proper Debian
package:
1. with a
I think putting the data itself into debian repository is problematic.
Regardless of any licensing issue, the shear amount of data is too great.
Better to let the professionals who are getting paid to manage the data (NCBI,
KEGG, etc.) and download directly from those sites. Pretty much all
well -- this issue is tangentially related to the software: why should
we care about having Debian packages while there are CRAN, easy_install,
etc -- all those great tools to deploy software -- domain specific and
created by specialists. Although such comparison is a stretch, I think
it has its
Le Tue, Feb 15, 2011 at 05:35:07PM -0600, Scott Christley a écrit :
I like the getData effort. Have a set of data descriptors with information
about how/where to get data, then when requested performs the download. This
is very much the architecture I was thinking about. I see a number of
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