As it was already mention, about the filtering we presented at Baltimore this project : https://github.com/abims-sbr/galaxy-blastprivate <https://github.com/abims-sbr/galaxy-blastprivate>
And about the report, we also have something about that :https://github.com/abims-sbr/galaxy-blastvisu <https://github.com/abims-sbr/galaxy-blastvisu> But shame on us, there is a lot of dust on them. Although, if we can build a little group around this project, we are stil interesting in. Our goal was also to drop out our W3Blast server. 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 21 sept. 2017 à 13:50, SAPET, Frederic <frederic.sa...@biogemma.com> a > écrit : > > Hi Peter, > > Good idea, I will keep that in mind for other needs. > I'm not sure that it will be suitable for what I want to do. Users will have > to first import database to their history (yet another step as they ask me > for less, even the upload process is sometimes one step they would like to > avoid !) > > But it could be a way of achieving what I want, if Galaxy could get files (or > .loc files) from a data library, within the tool form itself ! > > Maybe I will create an issue on the Galaxy git in order to discuss about > that. I will be glad to help if something can be done. > > Maybe some explanations about the fact that my users ask me for "less steps". > I really want Galaxy to be the main tool of our analysis platform. > Right now I still maintain a plain old perl/php/CGI web interface. With a > blast tool (among a lot of others tools). This proprietary Blast interface is > really like you will find on NCBI or EBI sites. And you can quickly paste > your sequences, pick up a database, a Blast algorythm and then launch. Few > seconds later I have a 'htmlized' Blast report, with a nice picture. > This use case (is this sequence a part of this database ?) is still faster on > this plain old interface. And I afraid that I will have to keep it until they > found Galaxy better than it... > > Maybe it could be another (or two) idea(s) : the user can drag and drop his > file within the tool form, Galaxy will handle the creation of this file > within the history and then launch the tool. Or user can copy/paste a > sequence within a text-area, and Galaxy will handle the creation of a file > from these data within the history and then launch the tool. > This skips upload process. > > thank you again for sharing your ideas, it helps! > > Fred > > -----Message d'origine----- > De : Peter Cock [mailto:p.j.a.c...@googlemail.com] > Envoyé : mercredi 20 septembre 2017 12:37 > À : SAPET, Frederic <frederic.sa...@biogemma.com> > Cc : Laure QUINTRIC <laure.quint...@ifremer.fr>; Galaxy-dev > <galaxy-dev@lists.galaxyproject.org> > Objet : Re: [galaxy-dev] Displaying tool select list according to user > > Have you tried creating the BLAST databases as files in your history (by > running makeblastdb within Galaxy), and then importing them into a shared > data library (which can then be configured with role based permissions)? > > Peter > > > On Wed, Sep 20, 2017 at 9:39 AM, SAPET, Frederic > <frederic.sa...@biogemma.com> wrote: >> Hello Laure >> >> >> >> this idea cannot be applied in my use case. >> >> indeed I don’t want that users can choose which data to display. I >> want to hide some data based on their name/group/address (anything >> that can be useful to clasify my users). >> >> >> >> Thank you for sharing your ideas :) >> >> >> >> Fred >> >> De : Laure QUINTRIC [mailto:laure.quint...@ifremer.fr] >> Envoyé : mercredi 13 septembre 2017 13:54 À : Peter Cock >> <p.j.a.c...@googlemail.com>; SAPET, Frederic >> <frederic.sa...@biogemma.com> >> >> >> Cc : Galaxy-dev <galaxy-dev@lists.galaxyproject.org> >> Objet : Re: [galaxy-dev] Displaying tool select list according to user >> >> >> >> A workaround would be to do this : >> >> - first, create a tool which will output a tabular loc file with all >> the custom banks for the connected user. >> - then add in the ncbi_blast wrapper a select list with the attribute >> from_dataset to load the loc file generated by the previous tool : >> see the example here : >> https://docs.galaxyproject.org/en/latest/dev/schema.html#from-dataset >> >> I have something like this in the ncbi_blast tool: >> <param name="userdb_loc_file" type="data" format="tabular" >> label="My custom dbs"/> >> <param name="custom_db" type="select" size="120" optional="true" >> multiple="true" display="checkboxes" label="Select our custom db"> >> <options from_dataset="userdb_loc_file"> >> <column name="value" index="0"/> >> <column name="name" index="1"/> >> <column name="path" index="2"/> >> </options> >> >> and I set in param userdb_loc_file the loc file which is in my history >> and looks like this : >> NCBI_nt<tab>NCBI_nt >> 2017-05-19<tab>/path/to/biobanks/n/NCBI_nt/current/NCBI_nt/NCBI_nt >> >> Laure >> >> Le 12/09/2017 à 17:25, Peter Cock a écrit : >> >> Thanks Fred, >> >> >> >> That's the previous discussion I was trying to find - >> >> sadly no clear solution but some ideas to explore. >> >> >> >> It does seem filtering example.loc by user or role >> >> is not a niche request. I wonder if this could be >> >> linked to the Galaxy data library permissions >> >> structure as a way to manage the access rights? >> >> >> >> Peter >> >> >> >> On Tue, Sep 12, 2017 at 4:20 PM, SAPET, Frederic >> <frederic.sa...@biogemma.com> wrote: >> >> Hi Laure, >> >> >> >> There are others users (including me! ) that need this kind of function : >> >> http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html >> >> >> >> @Galaxy team: >> >> Do we need to add an issue in GitHub ? >> >> Do you think that it could be enabled one day ? >> >> >> >> I think this something that could be nice to develop ! >> >> I would be glad to help. >> >> >> >> Thank a lot >> >> >> >> Fred >> >> >> >> De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De >> la part de Peter Cock Envoyé : mardi 12 septembre 2017 14:56 À : Laure >> QUINTRIC <laure.quint...@ifremer.fr> Cc : Galaxy-dev >> <galaxy-dev@lists.galaxyproject.org> >> Objet : Re: [galaxy-dev] Displaying tool select list according to user >> >> >> >> Hi Laure, >> >> >> >> I don't think there is any easy to use mechanism for this in Galaxy. >> >> Unfortunately Galaxy loads all the *.loc files at startup and treats >> >> them as global values available to all users equally. >> >> >> >> I can't find the email thread, but I recall someone previously trying >> >> to do something with a single large example.loc file for all users >> >> but with an extra column for filtering by account name. I forget if >> >> they got these changes to work or not. >> >> >> >> Assuming you only have a few separate versions of the example.loc >> >> file, you could create copies of the BLAST wrapper XML file which >> >> use the specific *.loc file - and then restrict the tool by user? >> >> >> >> In either case at a minimum you would have to maintain local >> >> changes to the BLAST wrappers (and potentially changes to >> >> Galaxy itself), which is not a good situation. >> >> >> >> Peter >> >> >> >> On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC >> <laure.quint...@ifremer.fr> >> wrote: >> >> Hello Galaxy users, >> >> I try to figure out how I can display a select list into a galaxy tool >> according to the connected user. >> >> I have several .loc files containing the paths for custom blast >> databases I have created for several users (user1.loc, user2.loc, and >> so on). I would like the blast tool to display the specific databases >> for the connected user >> (user1 or user2). >> >> Any idea on how to proceed ? >> Regards, >> Laure >> >> >> ___________________________________________________________ >> 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/ >> >> >> >> >> >> >> >> -- >> >> Laure QUINTRIC >> >> IDM-RIC - Cellule Bio-informatique >> >> 02 98 22 49 11 > ___________________________________________________________ > 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/
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