Search box in tools menu / uncomplete wrappers list

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Search box in tools menu / uncomplete wrappers list

Sarah Maman-3


Hello,


When I’m searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description.

Could you please help us to understand why ?


Thanks,

Sarah Maman




_____________________________
Sarah Maman

Bioinformatique/Bioinformatics

INRA | SIGENAE | GenPhySE

Centre Inra Occitanie-Toulouse
Tél. : +33(0)5.61.28.57.08

_____________________________

Chemin de Borde Rouge CS 52627
31326 Castanet Tolosan cedex

www.toulouse.inra.fr

Suivez-nous sur Twitter !


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Re: Search box in tools menu / uncomplete wrappers list

Martin Čech
Hi Sarah,

toolpanel search in Galaxy is configurable. Due to limited space the default number of results shown is 20 so if there are more you are not going to see them. You can also change weights of various search attributes or use ngram search. Please see the config options explained in the sample here: https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147

Please, let us know if you have more questions.

Thanks,

Martin

On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman <[hidden email]> wrote:


Hello,


When I’m searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description.

Could you please help us to understand why ?


Thanks,

Sarah Maman




_____________________________
Sarah Maman

Bioinformatique/Bioinformatics

INRA | SIGENAE | GenPhySE

Centre Inra Occitanie-Toulouse
Tél. : <a href="tel:+33%205%2061%2028%2057%2008" value="+33561285708" target="_blank">+33(0)5.61.28.57.08

_____________________________

Chemin de Borde Rouge CS 52627
31326 Castanet Tolosan cedex

www.toulouse.inra.fr

Suivez-nous sur Twitter !

___________________________________________________________
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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Re: Search box in tools menu / uncomplete wrappers list

Sarah Maman-3

Hello Martin,


Thanks a lot. I increased  tool_search_limit to 25 (20 by default) in galaxy.ini file and my toolpanel search is now well configurated.


Have a nice day,

Sarah


_____________________________
Sarah Maman

Bioinformatique/Bioinformatics

INRA | SIGENAE | GenPhySE

Centre Inra Occitanie-Toulouse
Tél. : +33(0)5.61.28.57.08

_____________________________

Chemin de Borde Rouge CS 52627
31326 Castanet Tolosan cedex

www.toulouse.inra.fr

Suivez-nous sur Twitter !


De : Martin Čech <[hidden email]>
Envoyé : vendredi 9 novembre 2018 18:13
À : Sarah Maman
Cc : [hidden email]
Objet : Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list
 
Hi Sarah,

toolpanel search in Galaxy is configurable. Due to limited space the default number of results shown is 20 so if there are more you are not going to see them. You can also change weights of various search attributes or use ngram search. Please see the config options explained in the sample here: https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147

Please, let us know if you have more questions.

Thanks,

Martin

On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman <[hidden email]> wrote:


Hello,


When I’m searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description.

Could you please help us to understand why ?


Thanks,

Sarah Maman




_____________________________
Sarah Maman

Bioinformatique/Bioinformatics

INRA | SIGENAE | GenPhySE

Centre Inra Occitanie-Toulouse
Tél. : <a href="tel:&#43;33%205%2061%2028%2057%2008" value="&#43;33561285708" target="_blank">+33(0)5.61.28.57.08

_____________________________

Chemin de Borde Rouge CS 52627
31326 Castanet Tolosan cedex

www.toulouse.inra.fr

Suivez-nous sur Twitter !

___________________________________________________________
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/

___________________________________________________________
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:
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Re: Search box in tools menu / uncomplete wrappers list

Matthias Bernt
In reply to this post by Sarah Maman-3
Hi,

I observed similar Problems on my Galaxy. But I think not all cases can
be explained by Martins answer. For instance, if I search for "hisat" I
don't get any result, but HISAT2 is definitely installed.

Cheers,
Matthias


> Message: 1
> Date: Fri, 9 Nov 2018 15:54:16 +0000
> From: Sarah Maman <[hidden email]>
> To: "[hidden email]"
> <[hidden email]>
> Subject: [galaxy-dev] Search box in tools menu / uncomplete wrappers
> list
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hello,
>
>
> When I'm searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description.
>
> Could you please help us to understand why ?
>
>
> Thanks,
>
> Sarah Maman
>
>
>
>
> _____________________________
> Sarah Maman
>
> Bioinformatique/Bioinformatics
>
> INRA | SIGENAE | GenPhySE
>
> Centre Inra Occitanie-Toulouse
> Tél. : +33(0)5.61.28.57.08
>
> _____________________________
>
> Chemin de Borde Rouge CS 52627
> 31326 Castanet Tolosan cedex
>
> www.toulouse.inra.fr<http://www.toulouse.inra.fr/>
>
> Suivez-nous sur Twitter !
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20181109/5edcc351/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 9 Nov 2018 12:13:53 -0500
> From: Martin Čech <[hidden email]>
> To: Sarah Maman <[hidden email]>
> Cc: "[hidden email]"
> <[hidden email]>
> Subject: Re: [galaxy-dev] Search box in tools menu / uncomplete
> wrappers list
> Message-ID:
> <CAHKBquHddNfir=[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sarah,
>
> toolpanel search in Galaxy is configurable. Due to limited space the
> default number of results shown is 20 so if there are more you are not
> going to see them. You can also change weights of various search attributes
> or use ngram search. Please see the config options explained in the sample
> here:
> https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147
>
> Please, let us know if you have more questions.
>
> Thanks,
>
> Martin
>
> On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman <[hidden email]> wrote:
>
>>
>> Hello,
>>
>>
>> When I’m searching a keyword in the « search » box in left « tools » menu,
>> results are sometimes false because the wrappers' list generated by the
>> query thanks to a keyword is not full, some tools are missing. In fact,
>> some wrappers are not listed even if the keyword is in the tool name and/or
>> the tool description.
>>
>> Could you please help us to understand why ?
>>
>>
>> Thanks,
>>
>> Sarah Maman
>>
>>
>>
>>
>>
>> *_____________________________ **Sarah* *Maman*
>>
>> Bioinformatique/Bioinformatics
>>
>> INRA | SIGENAE | GenPhySE
>>
>>
>> *Centre Inra Occitanie-Toulouse *Tél. : +33(0)5.61.28.57.08
>> <+33%205%2061%2028%2057%2008>
>>
>> *_____________________________*
>>
>> Chemin de Borde Rouge CS 52627
>> 31326 Castanet Tolosan cedex
>>
>> *www.toulouse.inra.fr* <http://www.toulouse.inra.fr/>
>>
>> *Suivez-nous sur Twitter !*
>> ___________________________________________________________
>> 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/
> -------------- next part --------------
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>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> https://lists.galaxyproject.org/listinfo/galaxy-dev
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
> ------------------------------
>
> End of galaxy-dev Digest, Vol 149, Issue 3
> ******************************************
>

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: Search box in tools menu / uncomplete wrappers list

E. Rasche
Hi Matthias, Sarah,

UseGalaxy.eu had noticed this issue a while back. We filed
https://github.com/galaxyproject/galaxy/issues/6724

And it was fixed in
https://github.com/galaxyproject/galaxy/pull/6737

You may need to update to the latest 18.05/18.09 (and possibly rebuild
client)

Cheers,
Helena

On 2018-11-12 11:17, Matthias Bernt wrote:

> Hi,
>
> I observed similar Problems on my Galaxy. But I think not all cases can be
> explained by Martins answer. For instance, if I search for "hisat" I don't
> get any result, but HISAT2 is definitely installed.
>
> Cheers,
> Matthias
>
>
> >Message: 1
> >Date: Fri, 9 Nov 2018 15:54:16 +0000
> >From: Sarah Maman <[hidden email]>
> >To: "[hidden email]"
> > <[hidden email]>
> >Subject: [galaxy-dev] Search box in tools menu / uncomplete wrappers
> > list
> >Message-ID: <[hidden email]>
> >Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> >Hello,
> >
> >
> >When I'm searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description.
> >
> >Could you please help us to understand why ?
> >
> >
> >Thanks,
> >
> >Sarah Maman
> >
> >
> >
> >
> >_____________________________
> >Sarah Maman
> >
> >Bioinformatique/Bioinformatics
> >
> >INRA | SIGENAE | GenPhySE
> >
> >Centre Inra Occitanie-Toulouse
> >Tél. : +33(0)5.61.28.57.08
> >
> >_____________________________
> >
> >Chemin de Borde Rouge CS 52627
> >31326 Castanet Tolosan cedex
> >
> >www.toulouse.inra.fr<http://www.toulouse.inra.fr/>
> >
> >Suivez-nous sur Twitter !
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20181109/5edcc351/attachment-0001.html>
> >
> >------------------------------
> >
> >Message: 2
> >Date: Fri, 9 Nov 2018 12:13:53 -0500
> >From: Martin Čech <[hidden email]>
> >To: Sarah Maman <[hidden email]>
> >Cc: "[hidden email]"
> > <[hidden email]>
> >Subject: Re: [galaxy-dev] Search box in tools menu / uncomplete
> > wrappers list
> >Message-ID:
> > <CAHKBquHddNfir=[hidden email]>
> >Content-Type: text/plain; charset="utf-8"
> >
> >Hi Sarah,
> >
> >toolpanel search in Galaxy is configurable. Due to limited space the
> >default number of results shown is 20 so if there are more you are not
> >going to see them. You can also change weights of various search attributes
> >or use ngram search. Please see the config options explained in the sample
> >here:
> >https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147
> >
> >Please, let us know if you have more questions.
> >
> >Thanks,
> >
> >Martin
> >
> >On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman <[hidden email]> wrote:
> >
> >>
> >>Hello,
> >>
> >>
> >>When I’m searching a keyword in the « search » box in left « tools » menu,
> >>results are sometimes false because the wrappers' list generated by the
> >>query thanks to a keyword is not full, some tools are missing. In fact,
> >>some wrappers are not listed even if the keyword is in the tool name and/or
> >>the tool description.
> >>
> >>Could you please help us to understand why ?
> >>
> >>
> >>Thanks,
> >>
> >>Sarah Maman
> >>
> >>
> >>
> >>
> >>
> >>*_____________________________ **Sarah* *Maman*
> >>
> >>Bioinformatique/Bioinformatics
> >>
> >>INRA | SIGENAE | GenPhySE
> >>
> >>
> >>*Centre Inra Occitanie-Toulouse *Tél. : +33(0)5.61.28.57.08
> >><+33%205%2061%2028%2057%2008>
> >>
> >>*_____________________________*
> >>
> >>Chemin de Borde Rouge CS 52627
> >>31326 Castanet Tolosan cedex
> >>
> >>*www.toulouse.inra.fr* <http://www.toulouse.inra.fr/>
> >>
> >>*Suivez-nous sur Twitter !*
> >>___________________________________________________________
> >>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/
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20181109/0c7c7b43/attachment-0001.html>
> >
> >------------------------------
> >
> >Subject: Digest Footer
> >
> >_______________________________________________
> >galaxy-dev mailing list
> >[hidden email]
> >https://lists.galaxyproject.org/listinfo/galaxy-dev
> >
> >To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> >
> >------------------------------
> >
> >End of galaxy-dev Digest, Vol 149, Issue 3
> >******************************************
> >
>
> --
>
> -------------------------------------------
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> [hidden email], www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
> Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> -------------------------------------------
> ___________________________________________________________
> 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/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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