automatically adding fasta files to "built-in" databases and selecting files questions

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automatically adding fasta files to "built-in" databases and selecting files questions

Nikhil Joshi-2
Hi all,

We have a local install of Galaxy that we use for testing for our bioinformatics courses. I am creating some new tool interfaces for the install. I want to create a tool that will allow a user to automatically add a fasta database to the "built-in" databases (without needing to reboot the server). Is this possible?

Along with that issue is that the number of databases for this tool can number in the thousands. Is there a way to easily search the built-in databases for the database you are looking for, and then use that database in a tool? Right now, it is an enormous drop down list which is really annoying and unwieldy.

Finally, these tools can take multiple input files, but I really don't like the way galaxy handles that where you have to continually click on "Add another file". Is there a method or work-around in galaxy where you can have a multi-file select?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

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Re: automatically adding fasta files to "built-in" databases and selecting files questions

Hans-Rudolf Hotz
Hi Nik

I don't think there is a solution out of the box for all of this, but I
will try to give you some pointers - others might have different or even
better suggestions (my suggestion are very 'hacky'). Let me answer your
questions in reverse order:

- Instead of using "Add another file", display all your files as
   checkboxes:

   type="select" display="checkboxes" multiple="true"

   you then get a comma separated string with containing all the
   selected files

   one option to populate the checkboxes is using "dynamic_options" or
   "from_file" which both allow you to read the list of files stored in
    a extra table


- A list with thousands of files to choose from is obviously not very
   handy. You can build a tree where you can open and collapse
   individual branches using

   type="drill_down" together with "from_file"

   Or as an alternative to searching, you can use "conditional" and then
   only display part of the list.


- you can write a little tool, which allows people to select a
   history item (or uploads a new file) which is then stored at a new
   location (outside the galaxy database directory). In a second step,
   this tool adds the item to the table which is read by
   "dynamic_options" or "from_file". Using "from_file" would require a
   restart, but a tool reload.


I hope you get a few ideas out of this

Regards, Hans-Rudolf



On 04/09/2014 04:34 AM, Nikhil Joshi wrote:

> Hi all,
>
> We have a local install of Galaxy that we use for testing for our
> bioinformatics courses. I am creating some new tool interfaces for the
> install. I want to create a tool that will allow a user to automatically
> add a fasta database to the "built-in" databases (without needing to
> reboot the server). Is this possible?
>
> Along with that issue is that the number of databases for this tool can
> number in the thousands. Is there a way to easily search the built-in
> databases for the database you are looking for, and then use that
> database in a tool? Right now, it is an enormous drop down list which is
> really annoying and unwieldy.
>
> Finally, these tools can take multiple input files, but I really don't
> like the way galaxy handles that where you have to continually click on
> "Add another file". Is there a method or work-around in galaxy where you
> can have a multi-file select?
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: automatically adding fasta files to "built-in" databases and selecting files questions

Hans-Rudolf Hotz
Hi Nik

Have a look at the "Profile Annotations" tool
(~/tools/annotation_profiler/annotation_profiler.xml)

and the file ~/tool-data/annotation_profiler_options.xml


Regards, Hans-Rudolf




On 04/19/2014 12:48 AM, Nikhil Joshi wrote:

> Hi Hans,
>
> Thanks for your response. I am trying to get just one part working right
> now, and that is the selecting of a database file. You suggest using a
> drill_down, but I can't seem to find good documentation on how to get it
> to work. I have been looking at the annotation_profiler tool to get
> ideas, but it still is unclear to me. Can you give me a simple example
> of how one would create the file that the drill_down would use and then
> how to use that file?
>
> - Nik.
>
>
>
> On Wed, Apr 9, 2014 at 1:13 AM, Hans-Rudolf Hotz <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Nik
>
>     I don't think there is a solution out of the box for all of this,
>     but I will try to give you some pointers - others might have
>     different or even better suggestions (my suggestion are very
>     'hacky'). Let me answer your questions in reverse order:
>
>     - Instead of using "Add another file", display all your files as
>        checkboxes:
>
>        type="select" display="checkboxes" multiple="true"
>
>        you then get a comma separated string with containing all the
>        selected files
>
>        one option to populate the checkboxes is using "dynamic_options" or
>        "from_file" which both allow you to read the list of files stored in
>         a extra table
>
>
>     - A list with thousands of files to choose from is obviously not very
>        handy. You can build a tree where you can open and collapse
>        individual branches using
>
>        type="drill_down" together with "from_file"
>
>        Or as an alternative to searching, you can use "conditional" and then
>        only display part of the list.
>
>
>     - you can write a little tool, which allows people to select a
>        history item (or uploads a new file) which is then stored at a new
>        location (outside the galaxy database directory). In a second step,
>        this tool adds the item to the table which is read by
>        "dynamic_options" or "from_file". Using "from_file" would require a
>        restart, but a tool reload.
>
>
>     I hope you get a few ideas out of this
>
>     Regards, Hans-Rudolf
>
>
>
>
>     On 04/09/2014 04:34 AM, Nikhil Joshi wrote:
>
>         Hi all,
>
>         We have a local install of Galaxy that we use for testing for our
>         bioinformatics courses. I am creating some new tool interfaces
>         for the
>         install. I want to create a tool that will allow a user to
>         automatically
>         add a fasta database to the "built-in" databases (without needing to
>         reboot the server). Is this possible?
>
>         Along with that issue is that the number of databases for this
>         tool can
>         number in the thousands. Is there a way to easily search the
>         built-in
>         databases for the database you are looking for, and then use that
>         database in a tool? Right now, it is an enormous drop down list
>         which is
>         really annoying and unwieldy.
>
>         Finally, these tools can take multiple input files, but I really
>         don't
>         like the way galaxy handles that where you have to continually
>         click on
>         "Add another file". Is there a method or work-around in galaxy
>         where you
>         can have a multi-file select?
>
>         - Nik.
>
>         --
>         Nikhil Joshi
>         Bioinformatics Analyst/Programmer
>         UC Davis Bioinformatics Core
>         http://bioinformatics.ucdavis.__edu/
>         <http://bioinformatics.ucdavis.edu/>
>         najoshi -at- ucdavis -dot- edu
>         530.752.2698 <tel:530.752.2698> (w)
>
>
>         _____________________________________________________________
>         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:
>         http://lists.bx.psu.edu/
>
>         To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/__search/mailinglists/
>         <http://galaxyproject.org/search/mailinglists/>
>
>
>
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/