[galaxy-dev] error installing dependency for tool shed repository.
I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084 ___ 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/
Re: [galaxy-dev] error installing dependency for tool shed repository.
Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. On 2013-08-21 19:12, Curt Palm wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error installing dependency for tool shed repository.
Hi Dave, I made changes giving the suggestions of Ross, I got a different error and that gave me insight as to what was going on. I uploaded new xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=shell_commandexport PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python amp;amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency And this worked for me. I'm thinking you may have downloaded after I made the changes. -Curt On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. Try moving the action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action line so it's the one before action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action I think I've been bitten by this - it seems download_by_url changes the current path but only temporarily so you need to run setup.py immediately as the next step? If this works, please confirm to the entire list - I'm sending this to you just in case I'm full of it :) On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm cp...@ingenuity.com wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J On 2013-08-21 19:12, Curt Palm wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/ requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City,
Re: [galaxy-dev] error installing dependency for tool shed repository.
Curt, I'm happy to hear that everything is now working. If you encounter any further issues, please don't hesitate to contact us. --Dave B. On 2013-08-21 21:31, Curt Palm wrote: Hi Dave, I made changes giving the suggestions of Ross, I got a different error and that gave me insight as to what was going on. I uploaded new xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=shell_commandexport PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python amp;amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency And this worked for me. I'm thinking you may have downloaded after I made the changes. -Curt On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. Try moving the action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action line so it's the one before action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action I think I've been bitten by this - it seems download_by_url changes the current path but only temporarily so you need to run setup.py immediately as the next step? If this works, please confirm to the entire list - I'm sending this to you just in case I'm full of it :) On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm cp...@ingenuity.com wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? ___ 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/
