Hi again all So I uploaded a tool with a single dependency to python2.7.10 to the testtoolshed (https://testtoolshed.g2.bx.psu.edu/view/ulfschaefer/filter_vcf/d0afc9c121a5).
Then I try to install it back on my test Galaxy instance. There are some error messages when trying to install the dependencies of package_python_2_7_10 (e.g. package readline_6_3 or package_gdbm_1_11) These seem to be resolved when I go into the admin interface and uninstall and reinstall these one by one. However, when I try to reinstall the package_python_2_7_10 itself after uninstalling it, I get this: Error - <type 'exceptions.TypeError'>: coercing to Unicode: need string or buffer, NoneType found URL: http://testgalaxy/admin_toolshed/manage_tool_dependencies?repository_id=d071e794759ab192&operation=install File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 92 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 891 in manage_tool_dependencies status=status ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 92 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 494 in initiate_tool_dependency_installation tool_shed_repository.repo_path( trans.app ) ) File '/home/galaxy/galaxy-dist/lib/tool_shed/util/hg_util.py', line 138 in get_config_from_disk for root, dirs, files in os.walk( relative_install_dir ): File '/usr/lib64/python2.6/os.py', line 276 in walk names = listdir(top) TypeError: coercing to Unicode: need string or buffer, NoneType found What have I done wrong so that relative_install_dir is not set. Wasn't really a problem when I installed the other dependencies. Any help would be appreciated. I tried switching if off and on again, but unfortunately it did not help. Thanks Ulf On 01/12/15 16:07, Martin Čech wrote: > Hi Ulf, > > you most probably want your tool to depend on package_python_2_7_10 from > the iuc (it will ensure your tool has access to 2.7.10 no matter what > python the Galaxy executing your tool is using) > > The package is being developed here > https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_10 > and > is available at the MTS here > https://toolshed.g2.bx.psu.edu/view/iuc/package_python_2_7_10/73631e818d3d > > You will need to add to your wrapper's xml something like: > > <requirements> > <requirement type="package" version="2.7.10">python</requirement> > </requirements> > > And you have to include tool_dependencies.xml file which will look > something like: > > <?xml version="1.0"?> > <tool_dependency> > <package name="python" version="2.7.10"> > <repository name="package_python_2_7_10" owner="iuc" > prior_installation_required="True" /> > </package> > </tool_dependency> > > Please let me know if you have more questions. > > M. > > On Tue, Dec 1, 2015 at 10:54 AM Ulf Schaefer <ulf.schae...@phe.gov.uk > <mailto:ulf.schae...@phe.gov.uk>> wrote: > > Dear all > > I have a Python script that I would like to publish to the tool shed. It > has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML). > It also needs a Python version 2.7<=X<3, which is not available per > default everywhere. > > Firstly, how do I specify these dependencies in the tool > <requirements> tag? > > And secondly, once I have a correct set of tool definition files with > tests and test data, how do I best get it onto the tool shed? > > I had a look through the wiki and the planemo documentation. > Unfortunately how to handle these dependencies did not become > immediately obvious (to me). > > Thanks for any pointers and sorry if this has been answered some place I > did not look. > > Cheers > Ulf > > -- > Ulf Schaefer, PhD > Bioinformatics Scientist > Bioinformatics Unit - Infectious Disease Informatics > National Infection Service > Public Health England > 61 Colindale Ave, London NW9 5EQ > ulf.schae...@phe.gov.uk <mailto:ulf.schae...@phe.gov.uk> > http://www.gov.uk/phe > Protecting and improving the nation’s health > > ************************************************************************** > The information contained in the EMail and any attachments is > confidential and intended solely and for the attention and use of > the named addressee(s). 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