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 >>>> >>>> >>> -- >>> gpg key id: 4096R/326D8438 (pgp.mit.edu) >>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 >>> >>> >>> >>> -- >>> To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org >>> with a subject of "unsubscribe". Trouble? Contact >>> listmas...@lists.debian.org >>> Archive: http://lists.debian.org/4d5ba1ba.4060...@irisa.fr >>> >> > > -- > gpg key id: 4096R/326D8438 (pgp.mit.edu) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 > > > > -- > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: http://lists.debian.org/4d5c0249.3050...@irisa.fr > -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/af14615d-e4ec-4643-92a9-bce2f16cb...@mac.com
