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.cock@googlemail.com]
Envoyé : mercredi 20 septembre 2017 12:37
À : SAPET, Frederic <
frederic.sapet@biogemma.com>
Cc : Laure QUINTRIC <
Laure.Quintric@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.sapet@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.Quintric@ifremer.fr]
Envoyé : mercredi 13 septembre 2017 13:54 À : Peter Cock
<p.j.a.cock@googlemail.com>; SAPET, Frederic
<frederic.sapet@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.sapet@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-bounces@lists.galaxyproject.org] De
la part de Peter Cock Envoyé : mardi 12 septembre 2017 14:56 À : Laure
QUINTRIC <Laure.Quintric@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.Quintric@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
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Laure QUINTRIC
IDM-RIC - Cellule Bio-informatique
02 98 22 49 11
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