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_pyth... 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.Schaefer@phe.gov.uk <mailto:Ulf.Schaefer@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.schaefer@phe.gov.uk <mailto:ulf.schaefer@phe.gov.uk> http://www.gov.uk/phe Protecting and improving the nation’s health
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