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 <d...@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.borr...@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 >> >> ___________________________________________________________ >> 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/
