Creating a tool dependency packages

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Creating a tool dependency packages

Delisle Lucille

Dear Galaxy list,


I do not know if it is the right place to ask my question. I would like to create a tool dependency package for numexpr (a python library).

I tried to do it taking examples from different tool dependency packages from iuc for example.

I added my repository to the testtoolshed but when I tried to install it. The directory lib/python of my tool is empty.

My repository is : package_python_2_7_numexpr_2_6_2 

The big difference I see between the one from iuc and mine is the url:

For example, for pybigwig, the URL is : https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz

For my library numexpr I could not find such a url so I put the one I thought would be the good one: 

https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c


Thank you very much for your help,



Lucille Delisle, PhD
PostDoc Duboule Lab
Laboratory of Developmental Genomics
EPFL SV ISREC UPDUB
SV 2843
Station 19
CH-1015 Lausanne
Tel : +41 21 693 97 08

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Re: Creating a tool dependency packages

Delisle Lucille

I'm sorry,

I forgot to add the error log:


/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'setup_requires'
  warnings.warn(msg)
/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)
/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
  warnings.warn(msg)
Warning: Assuming default configuration (numexpr/tests/{setup_tests,setup}.py was not found)Traceback (most recent call last):
  File "setup.py", line 227, in <module>
    setup_package()
  File "setup.py", line 223, in setup_package
    setup(**metadata)
  File "/slipstream/galaxy/production/dependencies/numpy/1.9/iuc/package_python_2_7_numpy_1_9/5f2b261ffc5b/lib/python/numpy/distutils/core.py", line 169, in setup
    return old_setup(**new_attr)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/slipstream/galaxy/production/dependencies/numpy/1.9/iuc/package_python_2_7_numpy_1_9/5f2b261ffc5b/lib/python/numpy/distutils/command/install.py", line 62, in run
    r = self.setuptools_run()
  File "/slipstream/galaxy/production/dependencies/numpy/1.9/iuc/package_python_2_7_numpy_1_9/5f2b261ffc5b/lib/python/numpy/distutils/command/install.py", line 56, in setuptools_run
    self.do_egg_install()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/bdist_egg.py", line 151, in run
    self.run_command("egg_info")
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/slipstream/galaxy/production/dependencies/numpy/1.9/iuc/package_python_2_7_numpy_1_9/5f2b261ffc5b/lib/python/numpy/distutils/command/egg_info.py", line 11, in run
    _egg_info.run(self)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 180, in run
    self.find_sources()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 207, in find_sources
    mm.run()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 291, in run
    self.add_defaults()
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 320, in add_defaults
    sdist.add_defaults(self)
  File "/slipstream/galaxy/production/dependencies/python/2.7.10/iuc/package_python_2_7_10/a28e3c30828d/lib/python2.7/site-packages/setuptools/command/sdist.py", line 124, in add_defaults
    if not self.distribution.include_package_data:
AttributeError: NumpyDistribution instance has no attribute 'include_package_data'


Thank you very much,


Lucille Delisle, PhD
PostDoc Duboule Lab
Laboratory of Developmental Genomics
EPFL SV ISREC UPDUB
SV 2843
Station 19
CH-1015 Lausanne
Tel : +41 21 693 97 08

De : galaxy-dev <[hidden email]> de la part de Delisle Lucille <[hidden email]>
Envoyé : lundi 24 juillet 2017 11:58
À : [hidden email]
Objet : [galaxy-dev] Creating a tool dependency packages
 

Dear Galaxy list,


I do not know if it is the right place to ask my question. I would like to create a tool dependency package for numexpr (a python library).

I tried to do it taking examples from different tool dependency packages from iuc for example.

I added my repository to the testtoolshed but when I tried to install it. The directory lib/python of my tool is empty.

My repository is : package_python_2_7_numexpr_2_6_2 

The big difference I see between the one from iuc and mine is the url:

For example, for pybigwig, the URL is : https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz

For my library numexpr I could not find such a url so I put the one I thought would be the good one: 

https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c


Thank you very much for your help,



Lucille Delisle, PhD
PostDoc Duboule Lab
Laboratory of Developmental Genomics
EPFL SV ISREC UPDUB
SV 2843
Station 19
CH-1015 Lausanne
Tel : +41 21 693 97 08

___________________________________________________________
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/

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Re: Creating a tool dependency packages

Devon Ryan
In reply to this post by Delisle Lucille
You can remove everything starting with the "#" in the URL, though I
presume that's not the problem. Have a look in the installation log on
your machine, perhaps there's an error message somewhere in it.

More conveniently, though, numexpr-2.6.2 is available in conda-forge,
so if you use conda as a dependency resolver then you can skip
creating a tool dependency package. This saves a LOT of hassle, in my
experience.

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
<[hidden email]> wrote:

> Dear Galaxy list,
>
>
> I do not know if it is the right place to ask my question. I would like to
> create a tool dependency package for numexpr (a python library).
>
> I tried to do it taking examples from different tool dependency packages
> from iuc for example.
>
> I added my repository to the testtoolshed but when I tried to install it.
> The directory lib/python of my tool is empty.
>
> My repository is : package_python_2_7_numexpr_2_6_2
>
> The big difference I see between the one from iuc and mine is the url:
>
> For example, for pybigwig, the URL is :
> https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz
>
> For my library numexpr I could not find such a url so I put the one I
> thought would be the good one:
>
> https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c
>
>
> Thank you very much for your help,
>
>
>
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
>
> ___________________________________________________________
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: Creating a tool dependency packages

Delisle Lucille
Hello Devon,
Thank you very much for your quick answer. In fact in my tool_dependencies.xml I did not put the '#':
           <package sha256sum="6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705">
             https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz
           </package>
The log has been sent in a different e-mail (sorry).

I think the conda is a really good alternative but I did not know how to ask conda to resolve it.
In fact, I need numexpr to install another python library and I do not know how to write in this new package how to look for numexpr with conda.

Thanks again,

Lucille

Lucille Delisle, PhD
PostDoc Duboule Lab
Laboratory of Developmental Genomics
EPFL SV ISREC UPDUB
SV 2843
Station 19
CH-1015 Lausanne
Tel : +41 21 693 97 08

________________________________________
De : [hidden email] <[hidden email]> de la part de Devon Ryan <[hidden email]>
Envoyé : lundi 24 juillet 2017 12:06
À : Delisle Lucille
Cc : [hidden email]
Objet : Re: [galaxy-dev] Creating a tool dependency packages

You can remove everything starting with the "#" in the URL, though I
presume that's not the problem. Have a look in the installation log on
your machine, perhaps there's an error message somewhere in it.

More conveniently, though, numexpr-2.6.2 is available in conda-forge,
so if you use conda as a dependency resolver then you can skip
creating a tool dependency package. This saves a LOT of hassle, in my
experience.

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
<[hidden email]> wrote:

> Dear Galaxy list,
>
>
> I do not know if it is the right place to ask my question. I would like to
> create a tool dependency package for numexpr (a python library).
>
> I tried to do it taking examples from different tool dependency packages
> from iuc for example.
>
> I added my repository to the testtoolshed but when I tried to install it.
> The directory lib/python of my tool is empty.
>
> My repository is : package_python_2_7_numexpr_2_6_2
>
> The big difference I see between the one from iuc and mine is the url:
>
> For example, for pybigwig, the URL is :
> https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz
>
> For my library numexpr I could not find such a url so I put the one I
> thought would be the good one:
>
> https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c
>
>
> Thank you very much for your help,
>
>
>
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
>
> ___________________________________________________________
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: Creating a tool dependency packages

Devon Ryan
In general, see if the new package is available in conda-forge or
bioconda. If so, you just need to mention it in the requirements
section of the tool XML.
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Mon, Jul 24, 2017 at 12:21 PM, Delisle Lucille
<[hidden email]> wrote:

> Hello Devon,
> Thank you very much for your quick answer. In fact in my tool_dependencies.xml I did not put the '#':
>            <package sha256sum="6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705">
>              https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz
>            </package>
> The log has been sent in a different e-mail (sorry).
>
> I think the conda is a really good alternative but I did not know how to ask conda to resolve it.
> In fact, I need numexpr to install another python library and I do not know how to write in this new package how to look for numexpr with conda.
>
> Thanks again,
>
> Lucille
>
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
>
> ________________________________________
> De : [hidden email] <[hidden email]> de la part de Devon Ryan <[hidden email]>
> Envoyé : lundi 24 juillet 2017 12:06
> À : Delisle Lucille
> Cc : [hidden email]
> Objet : Re: [galaxy-dev] Creating a tool dependency packages
>
> You can remove everything starting with the "#" in the URL, though I
> presume that's not the problem. Have a look in the installation log on
> your machine, perhaps there's an error message somewhere in it.
>
> More conveniently, though, numexpr-2.6.2 is available in conda-forge,
> so if you use conda as a dependency resolver then you can skip
> creating a tool dependency package. This saves a LOT of hassle, in my
> experience.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: [hidden email]
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
> <[hidden email]> wrote:
>> Dear Galaxy list,
>>
>>
>> I do not know if it is the right place to ask my question. I would like to
>> create a tool dependency package for numexpr (a python library).
>>
>> I tried to do it taking examples from different tool dependency packages
>> from iuc for example.
>>
>> I added my repository to the testtoolshed but when I tried to install it.
>> The directory lib/python of my tool is empty.
>>
>> My repository is : package_python_2_7_numexpr_2_6_2
>>
>> The big difference I see between the one from iuc and mine is the url:
>>
>> For example, for pybigwig, the URL is :
>> https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz
>>
>> For my library numexpr I could not find such a url so I put the one I
>> thought would be the good one:
>>
>> https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c
>>
>>
>> Thank you very much for your help,
>>
>>
>>
>> Lucille Delisle, PhD
>> PostDoc Duboule Lab
>> Laboratory of Developmental Genomics
>> EPFL SV ISREC UPDUB
>> SV 2843
>> Station 19
>> CH-1015 Lausanne
>> Tel : +41 21 693 97 08
>>
>> ___________________________________________________________
>> 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:
  https://lists.galaxyproject.org/

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