Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread 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: dpr...@dpryan.com
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
<lucille.deli...@epfl.ch> wrote:
> Hello Devon,
> Thank you very much for your quick answer. In fact in my 
> tool_dependencies.xml I did not put the '#':
> sha256sum="6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705">
>  
> https://pypi.python.org/packages/31/43/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz
>
> 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 : dprya...@gmail.com <dprya...@gmail.com> de la part de Devon Ryan 
> <dpr...@dpryan.com>
> Envoyé : lundi 24 juillet 2017 12:06
> À : Delisle Lucille
> Cc : galaxy-dev@lists.galaxyproject.org
> 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: dpr...@dpryan.com
> 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
> <lucille.deli...@epfl.ch> 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/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/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"
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Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread Delisle Lucille 
Hello Devon,
Thank you very much for your quick answer. In fact in my tool_dependencies.xml 
I did not put the '#':
   
 
https://pypi.python.org/packages/31/43/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz
   
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 : dprya...@gmail.com <dprya...@gmail.com> de la part de Devon Ryan 
<dpr...@dpryan.com>
Envoyé : lundi 24 juillet 2017 12:06
À : Delisle Lucille
Cc : galaxy-dev@lists.galaxyproject.org
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: dpr...@dpryan.com
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
<lucille.deli...@epfl.ch> 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/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/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/

Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread Devon Ryan 
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: dpr...@dpryan.com
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
 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/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/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/

Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread 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 
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  de la part de 
Delisle