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 [email protected] > with a subject of "unsubscribe". Trouble? Contact [email protected] > Archive: http://lists.debian.org/[email protected] > -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
