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<https://testtoolshed.g2.bx.psu.edu/repository/browse_repository?id=23c1f7fed262740a> 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/31/43/7777ab9535c416faabd1865453389260fdad0... 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
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 <galaxy-dev-bounces@lists.galaxyproject.org> de la part de Delisle Lucille <lucille.delisle@epfl.ch> Envoyé : lundi 24 juillet 2017 11:58 À : galaxy-dev@lists.galaxyproject.org 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<https://testtoolshed.g2.bx.psu.edu/repository/browse_repository?id=23c1f7fed262740a> 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/31/43/7777ab9535c416faabd1865453389260fdad0... 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
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: dpryan@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.delisle@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/31/43/7777ab9535c416faabd1865453389260fdad0...
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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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/31/43/7777ab9535c416faabd1865453389260fdad0... </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 : dpryan79@gmail.com <dpryan79@gmail.com> de la part de Devon Ryan <dpryan@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: dpryan@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.delisle@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/31/43/7777ab9535c416faabd1865453389260fdad0...
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/
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: dpryan@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.delisle@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 '#': <package sha256sum="6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705"> https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad0... </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 : dpryan79@gmail.com <dpryan79@gmail.com> de la part de Devon Ryan <dpryan@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: dpryan@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.delisle@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/31/43/7777ab9535c416faabd1865453389260fdad0...
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/
participants (2)
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Delisle Lucille -
Devon Ryan