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
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
___________________________________________________________ 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/
Hi Peter, Thank you for your answer. Maybe I should try your option below : Le 12/09/2017 à 14:56, Peter Cock a écrit :
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.
But in this case, did you remember how to write the filter to match the extra column with the username to the connected account name ? as he $__user_id__ variable could not be user between <filter> tags ? Laure
Hi Laure, Maybe you can use the toolbox filtering [ https://galaxyproject.org/user-defined-toolbox-filters/ | https://galaxyproject.org/user-defined-toolbox-filters/ ] option to do that ? For example defining group of users and filtering toolbox regarding the user group... Cheers, Yvan De: "Laure Quintric" <Laure.Quintric@ifremer.fr> À: "Peter Cock" <p.j.a.cock@googlemail.com> Cc: "Galaxy-dev" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mardi 12 Septembre 2017 15:16:56 Objet: Re: [galaxy-dev] Displaying tool select list according to user Hi Peter, Thank you for your answer. Maybe I should try your option below : Le 12/09/2017 à 14:56, Peter Cock a écrit : 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. But in this case, did you remember how to write the filter to match the extra column with the username to the connected account name ? as he $__user_id__ variable could not be user between <filter> tags ? 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/ -- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Yvan Le Bras, PhD @Yvan2935 <°))))>< Projet 65 Millions d'observateurs Bureau 34, Station de Biologie marine BP 225, 29182 Concarneau CEDEX --- MNHN EGB/CESCO UMR 7204 43 rue Buffon 75005 PARIS tél.: +33 (0) 2 98 50 99 35 / +33 (0) 6.10.43.96.51 yvan.le-bras@mnhn.fr
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<mailto: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 ___________________________________________________________ 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/
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
___________________________________________________________ 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/
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 <mailto: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 <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 <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 <mailto:Laure.Quintric@ifremer.fr>> *Cc :* Galaxy-dev <galaxy-dev@lists.galaxyproject.org <mailto: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 <mailto: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
___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
-- Laure QUINTRIC IDM-RIC - Cellule Bio-informatique 02 98 22 49 11
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<mailto: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<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<mailto:Laure.Quintric@ifremer.fr>> Cc : Galaxy-dev <galaxy-dev@lists.galaxyproject.org<mailto: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<mailto: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 ___________________________________________________________ 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
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
___________________________________________________________ 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
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
___________________________________________________________ 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
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.sapet@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.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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On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic < frederic.sapet@biogemma.com> wrote:
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.
Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?
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...
We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.
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.
The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use. As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?
thank you again for sharing your ideas, it helps!
Fred
These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk. Peter
Hi, I have created 3 issues! Use different .loc files depending on user's parameters https://github.com/galaxyproject/galaxy/issues/4666 Access DataLibrary files from tool form https://github.com/galaxyproject/galaxy/issues/4667 File upload enhancement https://github.com/galaxyproject/galaxy/issues/4668 thank you Peter for pointing me out http://www.sequenceserver.com/ and of course as I also develop and maintain tools, I understand that all ‘craziest’ ideas cannot become a reality. Fred De : Peter Cock [mailto:p.j.a.cock@googlemail.com] Envoyé : jeudi 21 septembre 2017 14:46 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 On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <frederic.sapet@biogemma.com<mailto:frederic.sapet@biogemma.com>> wrote: 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. Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this? 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... We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater. 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. The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use. As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker? thank you again for sharing your ideas, it helps! Fred These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk. Peter
Hi Fred, Thanks a lot,, we are also intereted on that solution for our private database. Hope that we have any good news soon. Best regards, Mohamed 2017-09-21 16:01 GMT+02:00 SAPET, Frederic <frederic.sapet@biogemma.com>:
Hi,
I have created 3 issues!
Use different .loc files depending on user's parameters
https://github.com/galaxyproject/galaxy/issues/4666
Access DataLibrary files from tool form
https://github.com/galaxyproject/galaxy/issues/4667
File upload enhancement
https://github.com/galaxyproject/galaxy/issues/4668
thank you Peter for pointing me out http://www.sequenceserver.com/
and of course as I also develop and maintain tools, I understand that all ‘craziest’ ideas cannot become a reality.
Fred
*De :* Peter Cock [mailto:p.j.a.cock@googlemail.com] *Envoyé :* jeudi 21 septembre 2017 14:46 *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
On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic < frederic.sapet@biogemma.com> wrote:
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.
Good idea! I wonder if the Galaxy UI team can think of a good way to integrate this, which would make Shared Data library files available to any tool without the import to current history step? Can you reply with a link to the new GitHub issue for this?
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...
We used to run wwwBLAST locally for similar reasons. If I was trying to setup up something similar now, I'd look at http://www.sequenceserver.com/ for this - but making the Galaxy alternative easier to use would be neater.
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.
The Galaxy upload does now support drag and drop, so again in principle the Galaxy team might be able to extend the tool interface as well. The tool input's expected file formats could be used to guide the data-type sniffer and/or short list the choices shown to the use.
As well or instead, I could imagine having an upload icon associated with each tool input (again, creating a history item and selecting it for you)? This could take advantage of the fact that each tool's input parameter specifies the expected input file formats, so that might be mapped to known file extensions for a file picker?
thank you again for sharing your ideas, it helps!
Fred
These are great usability ideas you are putting forward here - as a Galaxy Tool Author they sound positive, but I cannot comment on how complicated it would be for the Galaxy UI team. Or indeed if the UI would actually be practical - or just overly complicate things which is always a risk.
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/
participants (6)
-
Gildas Le Corguillé -
Laure QUINTRIC -
Mohamed Kassam -
Peter Cock -
SAPET, Frederic -
Yvan Le Bras