Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
Hi Peter and Carlos, On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto carlos.borr...@gmail.com 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 Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already... I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry. Salve! Bjoern Peter ___ 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] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
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_virtualenvngs-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_virtualenvngs-tools==0.1.4/action --- action type=setup_virtualenvngs-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=e9d772a27c450e74changeset_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
Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
On Mon, Sep 16, 2013 at 4:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto carlos.borr...@gmail.com 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 Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already... Hi Peter, When I install my repository which has package_biopython_1_61 as a dependency, package_atlas_3_10 and package_lapack_3_4 show as Installed, missing tool dependencies(Grey). However package_biopython_1_61 shows as Installed(Green) and as far as I can tell everything is working with the tools depending on my repository. 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/
Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
Hi Carlos, On Mon, Sep 16, 2013 at 4:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto carlos.borr...@gmail.com 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 Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already... Hi Peter, When I install my repository which has package_biopython_1_61 as a dependency, package_atlas_3_10 and package_lapack_3_4 show as Installed, missing tool dependencies(Grey). However package_biopython_1_61 shows as Installed(Green) and as far as I can tell everything is working with the tools depending on my repository. actually that is correct if you did not manually deactivate CPU throttling. Can I kindly ask which OS do you use. On Ubuntu it can be deactivated automatically, on Fedora you need to be root. 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/
Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
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_virtualenvngs-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_virtualenvngs-tools==0.1.4/action --- action type=setup_virtualenvngs-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=e9d772a27c450e74changeset_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/
[galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
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_virtualenvngs-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_virtualenvngs-tools==0.1.4/action --- action type=setup_virtualenvngs-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=e9d772a27c450e74changeset_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/
Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
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_virtualenvngs-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_virtualenvngs-tools==0.1.4/action --- action type=setup_virtualenvngs-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=e9d772a27c450e74changeset_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:
Re: [galaxy-dev] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto carlos.borr...@gmail.com 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 Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already... Peter ___ 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] UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
On Mon, Sep 16, 2013 at 4:46 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Peter, When I install my repository which has package_biopython_1_61 as a dependency, package_atlas_3_10 and package_lapack_3_4 show as Installed, missing tool dependencies(Grey). However package_biopython_1_61 shows as Installed(Green) and as far as I can tell everything is working with the tools depending on my repository. actually that is correct if you did not manually deactivate CPU throttling. Can I kindly ask which OS do you use. On Ubuntu it can be deactivated automatically, on Fedora you need to be root. Sure, this is on Ubuntu 13.04. I would have to double check, but I believe I saw the same behavior on Centos 6.4. Best, --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/
