Hi Dylan, On 4/24/18 4:44 PM, Dylan Aïssi wrote: > Hi all, > > 2018-04-19 14:16 GMT+02:00 Andreas Tille <[email protected]>: >>> To answer Andreas, we, at OMICtools, could publish every month, the list of >>> new packages available in Debian Med on our blog : >>> https://omictools.com/blog, if you feel it can helps. > Thanks Fabien for this. :-) > >>> We just need a list of these tools and the corresponding OMICS_[0-9]{5} >>> RRID, if present. >> I think about some method to automatically create such a list. Steffen, >> would you volunteer to assemble it manually for the moment? > Steffen, did you already perform this? I quickly wrote a small script > to do this (attached). > It could be useful (... or not :-)) before to do a cleanest work. > > I also attached the generated list for March.
I do not see the overall context here. We have lists of packages with OMICtools assignments on the Debian side for which Andreas has crafted a script that accesses the UDD - it is here https://salsa.debian.org/blends-team/website/blob/master/misc/sql/edam.sh (also already preparing for EDAM annotation, but, well there are only 24h/day) and Fabien (and Jon of bio.tools+EDAM and Matúš of EDAM) is aware of it. There is an independently maintained list of assignments from OMICtools to Debian which the folks of OMICtools generate/maintain and kindly provided me with a CSV dump of these. My focus yet was on what we have on our task pages but I should also go through that list, add missing OMICtools references and extend our task pages where it fits. @Fabien, could you please send an updated public list of your OMICtools -> Debian mappings to the Debian Med mailing list? @us, to reflect our DFSG I always give all three major registries a chance and check if they have an entry for software to which I add an RRID of whatever source. That is why I also assign the "NA"s to indicate that I have looked. Concerning the "blog" entry I kind of like repeated news about our distribution. But what I would really like to see is a deeper integration of our packages within the regular OMICtools (bio.tools, SciCrunch, ...) web site to the degree that the OMICtools user can establish functional workflows more quickly. Any such competition between the OMICtools site and our task pages will point us to the packages that are used in workflows but not available as a package which will help us. And it will be a nice competition between BioConda, Docker images, our packages and whatever else the OMICtools folks will decide to reference. Best, Steffen
