Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?
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
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.cock@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
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.cock@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.cock@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
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Hi Gildas, When datatypes were moved to the Tool Shed, I think the idea was to eventually have only a core set of topic-neutral datatypes (plain text, tabular, etc) in Galaxy itself. That does seem sensible. I'm not quite sure why policy has returned to a larger centralised set - but limitations of the ToolShed like dependencies (for Python code imported directly into Galaxy), lack of versioning of datatypes, and better control of namespaces are likely part of this. I missed GCC2017 sadly. Even with a large set of datatypes included with Galaxy, it should be easy to hide/disable lots (e.g. for an image analysis Galaxy you would not want any of the sequence file formats). Peter P.S. Good point about EDAM, its been raised on the BLAST datatypes pull request: https://github.com/galaxyproject/galaxy/pull/2696 On Mon, Aug 1, 2016 at 9:27 PM, Gildas Le Corguillé <lecorguille@sb-roscoff.fr> wrote:
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
participants (2)
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Gildas Le Corguillé -
Peter Cock