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 PM, Scott Christley a écrit :
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 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 web interface, but interface is definitly a
plus....
Olivier
Le 2/16/11 5:53 PM, Scott Christley a écrit :
Hello,
I haven't followed the emails for biomaj packaging closely but I saw a number
of mentions that it may have to go into non-free? It does look like an
interesting technology that already has the capability to collect data from
various servers.
Scott
On Feb 16, 2011, at 4:06 AM, Olivier Sallou wrote:
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 provide an interface
(web or command-line) to get bank status (directory where available, additional
info etc...)
It is used in several bioinformatics labs worldwide.
What could be done for what you expect as to provide the Biomaj property files
as packages with postprocess dependencies (a depends Bowtie for example).
Package would put bank properties file and possible scripts in Biomaj.
Once Biomaj is officially packaged in Debian, I plan to package the existing
property files the community have developped around the tool (available on the
web site).
Those propery files would be an add-on package to Biomaj (for the moment we
have to manually put those in Biomaj bank directory).
Regards
Olivier
Le 2/15/11 9:24 PM, Scott Christley a écrit :
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 useful.
For example, If a user had high-throughput sequencing data that they need to
align to a genome. Now there is a tool available in debian called bowtie that
will do the job but the user needs to 1) download the genome and 2) generate
the bowtie index. Wouldn't it be great if you just type:
apt-get install bowtie-human-genome-index
which installed the genome and the pre-built indexes, then they could just run
bowtie directly.
Or another example is wanting to do your own BLAST searches, why not a package
that has the BLAST database indexes:
apt-get install BLAST-human-genome
What is nice is all of these data sets could be maintained in a global
directory space, like /usr/share, so all of the tools could share this space
preventing duplication, and made available to all users on the system. Right
now every user has to figure out how to manage their data individually which
can be difficult for biologists.
What do you think?
Scott
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