Problems with planemo functional tests

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Problems with planemo functional tests

Léo Biscassi
Hi Folks,
I tried follow this tutorial [1], but I have problems in execute the command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for perform functional tests, any suggestion? 
Bellow some images about this problem:

imagem1.jpg
Figure 1: Command

imagem2.jpg
Figure 2: Error

imagem3.jpg
Figure 3: Galaxy Path

Planemo's version is 0.23.0.


P.S: The command is utilized for same tool presented in tutorial.

Att.
--

___________________________________________________________
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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Problems with planemo functional tests

Björn Grüning-3
Hi,

maybe I'm mistaken something, its way to early here ... but you need to
specify a path to the tool you want to test.

For example:

planemo test /foo/bar/foo.xml

or to a directory full of tools.

planemo test /foo/bar

Hope this helps,
Bjoern

Am 03.03.2016 um 04:48 schrieb Léo Biscassi:

> Hi Folks,
> I tried follow this tutorial [1], but I have problems in execute the
> command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> perform functional tests, any suggestion?
> Bellow some images about this problem:
>
> imagem1.jpg
> *Figure 1: *Command
>
> imagem2.jpg
> *Figure 2:* Error
>
> imagem3.jpg
> *Figure 3: *Galaxy Path
>
> Planemo's version is 0.23.0.
>
> [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
>
> P.S: The command is utilized for same tool presented in tutorial.
>
> Att.
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
>
>
> ___________________________________________________________
> 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/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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Problems with planemo functional tests

Léo Biscassi
Hi, the command that you suggested not working, the same output is presented. I tested with the following commands:

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml --galaxy_root=/home/leobiscassi/programs/galaxy

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml

What is the influence of xUnit file in the process? I did the question because the warning message showing "Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown".

P.S.: My Galaxy instance is the latest stable version.

Best regards,

On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning <[hidden email]> wrote:
Hi,

maybe I'm mistaken something, its way to early here ... but you need to
specify a path to the tool you want to test.

For example:

planemo test /foo/bar/foo.xml

or to a directory full of tools.

planemo test /foo/bar

Hope this helps,
Bjoern

Am 03.03.2016 um 04:48 schrieb Léo Biscassi:
> Hi Folks,
> I tried follow this tutorial [1], but I have problems in execute the
> command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> perform functional tests, any suggestion?
> Bellow some images about this problem:
>
> imagem1.jpg
> *Figure 1: *Command
>
> imagem2.jpg
> *Figure 2:* Error
>
> imagem3.jpg
> *Figure 3: *Galaxy Path
>
> Planemo's version is 0.23.0.
>
> [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
>
> P.S: The command is utilized for same tool presented in tutorial.
>
> Att.
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
>
>
> ___________________________________________________________
> 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/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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Problems with planemo functional tests

Gildas Le Corguillé
Hi,

Do you still have the config/galaxy.ini.sample file unchanged ?

We observed this message when some .sample are missing or were modified.

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 3 mars 2016 à 07:31, Léo Biscassi <[hidden email]> a écrit :

Hi, the command that you suggested not working, the same output is presented. I tested with the following commands:

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml --galaxy_root=/home/leobiscassi/programs/galaxy

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml

What is the influence of xUnit file in the process? I did the question because the warning message showing "Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown".

P.S.: My Galaxy instance is the latest stable version.

Best regards,

On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning <[hidden email]> wrote:
Hi,

maybe I'm mistaken something, its way to early here ... but you need to
specify a path to the tool you want to test.

For example:

planemo test /foo/bar/foo.xml

or to a directory full of tools.

planemo test /foo/bar

Hope this helps,
Bjoern

Am 03.03.2016 um 04:48 schrieb Léo Biscassi:

> Hi Folks,
> I tried follow this tutorial [1], but I have problems in execute the
> command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> perform functional tests, any suggestion?
> Bellow some images about this problem:
>
> imagem1.jpg
> *Figure 1: *Command
>
> imagem2.jpg
> *Figure 2:* Error
>
> imagem3.jpg
> *Figure 3: *Galaxy Path
>
> Planemo's version is 0.23.0.
>
> [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
>
> P.S: The command is utilized for same tool presented in tutorial.
>
> Att.
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
>
>
> ___________________________________________________________
> 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/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:
 https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Problems with planemo functional tests

Léo Biscassi
Hi Gildas, thanks for the reply.
I had renamed galaxy.ini.sample file to galaxy.ini and performed my configurations to the server.
In fact, I created the file galaxy.ini.sample and command works fine!

Thanks a lot!

Best regards,

On Thu, Mar 3, 2016 at 5:46 AM Gildas Le Corguillé <[hidden email]> wrote:
Hi,

Do you still have the config/galaxy.ini.sample file unchanged ?

We observed this message when some .sample are missing or were modified.

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 3 mars 2016 à 07:31, Léo Biscassi <[hidden email]> a écrit :

Hi, the command that you suggested not working, the same output is presented. I tested with the following commands:

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml --galaxy_root=/home/leobiscassi/programs/galaxy

sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml

What is the influence of xUnit file in the process? I did the question because the warning message showing "Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown".

P.S.: My Galaxy instance is the latest stable version.

Best regards,

On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning <[hidden email]> wrote:
Hi,

maybe I'm mistaken something, its way to early here ... but you need to
specify a path to the tool you want to test.

For example:

planemo test /foo/bar/foo.xml

or to a directory full of tools.

planemo test /foo/bar

Hope this helps,
Bjoern

Am 03.03.2016 um 04:48 schrieb Léo Biscassi:

> Hi Folks,
> I tried follow this tutorial [1], but I have problems in execute the
> command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> perform functional tests, any suggestion?
> Bellow some images about this problem:
>
> imagem1.jpg
> *Figure 1: *Command
>
> imagem2.jpg
> *Figure 2:* Error
>
> imagem3.jpg
> *Figure 3: *Galaxy Path
>
> Planemo's version is 0.23.0.
>
> [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
>
> P.S: The command is utilized for same tool presented in tutorial.
>
> Att.
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
>
>
> ___________________________________________________________
> 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/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:
 https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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