testtoolshed : python-2.7 installation error

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testtoolshed : python-2.7 installation error

Geert Vandeweyer-4
Hi,

I get an installation error on the python 2.7 package in the test
toolshed. I used the 'contact owner' function, but wanted to mention it
here too, as there hasn't been reaction so far. Sorry for double posting
if so.

Error:

tar (child): 5.2.tar.bz2: Cannot open: No such file or directory

A similar error is in the Test run outputs. I believe it is related to
the following (unnecessary)  line in the tool_dependency.xml:

  <action type="change_directory">..</action>

located just after the download_file action for the 5.2.tar.bz2 file.

Best,

Geert

--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [hidden email]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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Re: testtoolshed : python-2.7 installation error

Peter Cock
Hi Geert,

Which tool is this?

Peter

On Thu, Aug 7, 2014 at 9:00 AM, Geert Vandeweyer
<[hidden email]> wrote:

> Hi,
>
> I get an installation error on the python 2.7 package in the test toolshed.
> I used the 'contact owner' function, but wanted to mention it here too, as
> there hasn't been reaction so far. Sorry for double posting if so.
>
> Error:
>
> tar (child): 5.2.tar.bz2: Cannot open: No such file or directory
>
> A similar error is in the Test run outputs. I believe it is related to the
> following (unnecessary)  line in the tool_dependency.xml:
>
>  <action type="change_directory">..</action>
>
> located just after the download_file action for the 5.2.tar.bz2 file.
>
> Best,
>
> Geert
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: [hidden email]
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>
> ___________________________________________________________
> 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/
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Re: testtoolshed : python-2.7 installation error

Björn Grüning-3
In reply to this post by Geert Vandeweyer-4
Hi Geert,

are you talking about the package_python_* repository?


Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer:
> Hi,
>
> I get an installation error on the python 2.7 package in the test
> toolshed. I used the 'contact owner' function, but wanted to mention it
> here too, as there hasn't been reaction so far. Sorry for double posting
> if so.

Oh this is interesting, because we did not get notified. It is from IUC
correct?

> Error:
>
> tar (child): 5.2.tar.bz2: Cannot open: No such file or directory
>
> A similar error is in the Test run outputs. I believe it is related to
> the following (unnecessary)  line in the tool_dependency.xml:
>
>   <action type="change_directory">..</action>

This can be. The cwd directory handling changed a lot in recent
versions, due to bugs. And for a few repositories we still have the
workarounds included.

I will upload a new version without this workaround and see if it passes.

> located just after the download_file action for the 5.2.tar.bz2 file.
>
> Best,
>
> Geert
>
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Re: testtoolshed : python-2.7 installation error

Geert Vandeweyer-4
sorry about that confusion :-)

Yes, I'm talking about the package_python_2.7 repository. The same error
is also present in the test runs of the package_python_3* repo.

Best,

Geert

On 08/07/2014 11:45 AM, Björn Grüning wrote:

> Hi Geert,
>
> are you talking about the package_python_* repository?
>
>
> Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer:
>> Hi,
>>
>> I get an installation error on the python 2.7 package in the test
>> toolshed. I used the 'contact owner' function, but wanted to mention it
>> here too, as there hasn't been reaction so far. Sorry for double posting
>> if so.
>
> Oh this is interesting, because we did not get notified. It is from
> IUC correct?
>
>> Error:
>>
>> tar (child): 5.2.tar.bz2: Cannot open: No such file or directory
>>
>> A similar error is in the Test run outputs. I believe it is related to
>> the following (unnecessary)  line in the tool_dependency.xml:
>>
>>   <action type="change_directory">..</action>
>
> This can be. The cwd directory handling changed a lot in recent
> versions, due to bugs. And for a few repositories we still have the
> workarounds included.
>
> I will upload a new version without this workaround and see if it passes.
>
>> located just after the download_file action for the 5.2.tar.bz2 file.
>>
>> Best,
>>
>> Geert
>>


--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [hidden email]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

___________________________________________________________
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: testtoolshed : python-2.7 installation error

Björn Grüning-3
Hi,

I updated the python wrappers. Depending on your Galaxy version it
should work now.

@Greg, we still have the error that  'contact owner' does not seem to
work :(

Cheers,
Bjoern

Am 07.08.2014 um 12:11 schrieb Geert Vandeweyer:

> sorry about that confusion :-)
>
> Yes, I'm talking about the package_python_2.7 repository. The same error
> is also present in the test runs of the package_python_3* repo.
>
> Best,
>
> Geert
>
> On 08/07/2014 11:45 AM, Björn Grüning wrote:
>> Hi Geert,
>>
>> are you talking about the package_python_* repository?
>>
>>
>> Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer:
>>> Hi,
>>>
>>> I get an installation error on the python 2.7 package in the test
>>> toolshed. I used the 'contact owner' function, but wanted to mention it
>>> here too, as there hasn't been reaction so far. Sorry for double posting
>>> if so.
>>
>> Oh this is interesting, because we did not get notified. It is from
>> IUC correct?
>>
>>> Error:
>>>
>>> tar (child): 5.2.tar.bz2: Cannot open: No such file or directory
>>>
>>> A similar error is in the Test run outputs. I believe it is related to
>>> the following (unnecessary)  line in the tool_dependency.xml:
>>>
>>>   <action type="change_directory">..</action>
>>
>> This can be. The cwd directory handling changed a lot in recent
>> versions, due to bugs. And for a few repositories we still have the
>> workarounds included.
>>
>> I will upload a new version without this workaround and see if it passes.
>>
>>> located just after the download_file action for the 5.2.tar.bz2 file.
>>>
>>> Best,
>>>
>>> Geert
>>>
>
>
___________________________________________________________
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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