Thanks!. I was actually in the process of testing this combination. I can confirm this error goes away when using a local instance of galaxy-central instead. On Mon, Sep 16, 2013 at 4:18 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Carlos,
The issue you're experiencing is due to features being added in the test tool shed that have not yet been accounted for in Galaxy's stable release to galaxy-dist. To resolve this issue, you'll need to be running a recently updated checkout of galaxy-central on the default branch, since the recently introduced features were added and are being handled in that branch.
--Dave B.
On 09/16/2013 03:57 PM, Carlos Borroto wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
On Mon, Sep 16, 2013 at 3:21 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
Hi,
I got this error when trying to install a repository I created defining a tool dependency. The odd thing is the exact same definition worked for the previous version of the same tool.
This is the repository failing to install, see full trace below: http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_5
This is the content of the only file in the repository: <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.61"> <repository name="package_biopython_1_61" owner="biopython" prior_installation_required="True" /> </package> <package name="ngs-tools" version="0.1.5"> <install version="1.0"> <actions> <action type="setup_virtualenv">ngs-tools==0.1.5</action> </actions> </install> </package> </tool_dependency>
This is the repository for the previous version of this package currently in the test toolshed and can be installed without issues: http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_4
Diff between tool_dependencies.xml files: $ diff package_ngs_tools_0_1_4/tool_dependencies.xml package_ngs_tools_0_1_5/tool_dependencies.xml 6c6 < <package name="ngs-tools" version="0.1.4"> ---
<package name="ngs-tools" version="0.1.5">
9c9 < <action type="setup_virtualenv">ngs-tools==0.1.4</action> ---
<action type="setup_virtualenv">ngs-tools==0.1.5</action>
Full trace: URL: http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=e9d772a27c450e74&changeset_revisions=df1454bc4a5e File '/home/cborroto/src/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/cborroto/src/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/cborroto/src/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/cborroto/src/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/cborroto/src/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/cborroto/src/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/home/cborroto/src/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 911 in prepare_for_install includes_tool_dependencies ) File '/home/cborroto/src/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 85 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) File '/home/cborroto/src/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 214 in get_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( rd_tup ) File '/home/cborroto/src/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 1183 in parse_repository_dependency_tuple prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
I clearly have to be missing something here. Any help? Thanks, Carlos
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