Hi all, If indeed, datatypes return within the Galaxy distribution, can we imagine propose different datatypes_conf.xml?
Galaxy isn’t anymore dedicated to NGS purpose. It is use also for metabolomics, proteomics, … So it could be great to propose 1 "common" list of datatypes (text, tabular, png, pdf, …) and n specific datatypes lists for the n scientific areas to reduce this huge list of datatypes proposed to the users. Maybe this selection should be based on edam ontology. As you know they are almost already annotated with edam_format and edam_data Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------ > Le 1 août 2016 à 18:41, Peter Cock <p.j.a.c...@googlemail.com> a écrit : > > I have a work-in-progress branch and pull request here, > https://github.com/peterjc/galaxy/tree/blast_datatypes > https://github.com/galaxyproject/galaxy/pull/2696 > > The Galaxy TravisCI tests looked fine. > > Peter > > On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> Dear all, >> >> I ran this past the IUC first, and the only comments were >> positive. >> >> Although I wasn't at GCC2017 to discuss this in person, >> I understand that the Galaxy Team now encourages >> widely used datatypes to be included in the main Galaxy >> repository, rather than distributed via the Tool Shed. >> >> To that end, would a pull request returning the BLAST >> datatypes and associated database *.loc files be welcome? >> >> These are currently on my GitHub repository here: >> https://github.com/peterjc/galaxy_blast/ >> >> And the datatypes are distributed via the Tool Shed here: >> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes >> >> Assuming this happens, we would need to phase out the >> tool shed version (but it will still be needed while older >> Galaxy instances are still running). >> >> Are there any pitfalls to worry about if the datatypes are >> already there with Galaxy and the tool shed version is >> installed on top? Or the tool shed version was installed >> but then Galaxy was updated to include the version >> bundled with Galaxy? >> >> Thanks, >> >> Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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