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vloux / ProteoRE

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Update bioconductor-org.*.eg.db to version 3.8.2 #244

Closed vloux closed 4 years ago

vloux commented 5 years ago

To fix #243 : dependencies problem in goprofiles.

To be coherent require also update in topgo , cluster_profiler, GO_terms_profiles_comparison

@yvandenb , @combesf is it Ok for you ?

yvandenb commented 5 years ago

Fully Agree => who to do this ?

combesf commented 5 years ago

ok for me for the update

vloux commented 5 years ago

@yves -> to test on goprofiles on dev-migale

yvandenb commented 5 years ago

Tested on http://migale.jouy.inra.fr/proteore/ History "update_BioCond_Org.eg.db" shared with VL and Flo. GoProfiles execution using "Lacombe" dataset Everything seems to be normal Green light to test TopGo and ClusterProfiler?

vloux commented 5 years ago

updated topGO & clusterProfiler -> to Test on dev-migale @combesf , I let you update GO_terms_profiles_comparison ?

yvandenb commented 5 years ago

Many thx Valentin..everything worked fine on my side, Flo? Of note, once deployed on Proteore.org, please update the "data sources" webpage: http://proteore.org/u/proteore/p/data-sources-2

combesf commented 5 years ago

It is in progress on my side ....

combesf commented 5 years ago

Updated GO_terms_profiles_comparison -> to test on Proteore.org (careful: betatools section) (updated tool is only on testTS for the moment)

combesf commented 5 years ago

Many thx Valentin..everything worked fine on my side, Flo? Of note, once deployed on Proteore.org, please update the "data sources" webpage: http://proteore.org/u/proteore/p/data-sources-2

--> done for topGO and clusterProfiler

yvandenb commented 5 years ago

Updated GO_terms_profiles_comparison -> to test on Proteore.org (careful: betatools section) Galaxy Version 2019.09.27 => Run failed image

combesf commented 5 years ago

@yvandenb I installed bioC-updated GO_terms_profile_comparison tool on proteore-migale --> it works for me on Human data

yvandenb commented 5 years ago

suite au TelCo lundi 7/10/2019: à déployer sur proteore.org + mise à jour de la page "Data sources": http://proteore.org/u/proteore/p/data-sources-2

combesf commented 5 years ago

I installed the new version (Sept 2019) of GO terms profiles comparison on peoteore.org (bêta tools section). It failed to run, error message = "DOSE package can't be loaded". The version called for DOSE pkg is 3.10.2, the same of the one for the "cluster_profiler" tool. Thus : @vloux could you please tell me if the update of "cluster_profiler" tool is OK on proteore [cluster_profiler tool also needs DOSE pkg] ? (I can install the updated cluster_profiler tool on proteore from the TS if you want)

vloux commented 4 years ago

Update of clusterprofiler, topGo done on proteore.org (at last !) Il let you test it thoroughly

yvandenb commented 4 years ago

Tests are OK...what about GoProfile tool ? Additional request: please, could you reorganize the tools panel accordingly ? i.e. these tools should be under the "GOterms analysis" section

vloux commented 4 years ago

GoProfile updated Reorganization done