Re: [galaxy-dev] adding tools using toolshed is not working
Hi Greg, Thanks a lot. This solved the issues I had. Greetz, Mattias On 06/15/2012 04:28 PM, Greg Von Kuster wrote: Hi Matthias, You uncovered an issue I recently introduced and which I've fixed in change set 7277:4a1389e037c6, which is now running on both public Galaxy tool sheds. Sorry for the back and forth on this - your line numbers in your paster log threw me since they were significantly different from mine. Thanks for reporting this problem! Greg Von Kuster On 06/15/2012 02:58 PM, Greg Von Kuster wrote: Hi Matthias, There is really nothing to configure in your Galaxy environment in order to use the public Galaxy tool sheds. Ideally, you should set the following configuration setting, but not setting it defaults to using the file named shed_tool_conf.xml for installed tools anyway. tool_config_files = tool_conf.xml,shed_tool_conf.xml The current Galaxy central repository tip is 7276:622fd4f0a437, which you should pull. This is the revision that the public tool sheds are using - they generally always run the Galaxy central tip revision. It's very possible that since you updated after 6 months of development, your repository has some issues. What are the results of the following commands? hg diff hg status hg verify hg summary On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote: Hi Greg, I guess something went wrong while update, because I updated to the latest changeset: hg tip | grep changeset changeset: 7262:4fbd05095ca7 Can it be because I the last time I updated was at least half a year ago and the toolshed integration has been implemented afterwards? So that I need to configure the toolshed before I can install something form the public one? Thanks! Mattias On 06/13/2012 05:43 PM, Greg Von Kuster wrote: Hello Mattias, Did you pull from the Galaxy central repo? The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed. Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine. Thanks, Greg Von Kuster On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: Hi, I just updated my local Galaxy installation to the latest version. I am trying out the feature to add tools directly from the toolshed, but this is not working. It results in this error: File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 481 in install_repository install_tool_dependencies=install_tool_dependencies ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 1228 in load_repository_contents dist_to_shed=False ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 342 in create_or_update_tool_shed_repository installed_changeset_revision=changeset_revision, NameError: global name 'changeset_revision' is not defined And my shed_tools_conf.xml looks like this: Should I put more configuration in this file? Any help is appreciated. Thanks! Mattias ___ 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/ ___ 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/
Re: [galaxy-dev] adding tools using toolshed is not working
Hi Matthias, You uncovered an issue I recently introduced and which I've fixed in change set 7277:4a1389e037c6, which is now running on both public Galaxy tool sheds. Sorry for the back and forth on this - your line numbers in your paster log threw me since they were significantly different from mine. Thanks for reporting this problem! Greg Von Kuster > On 06/15/2012 02:58 PM, Greg Von Kuster wrote: >> >> Hi Matthias, >> >> There is really nothing to configure in your Galaxy environment in order to >> use the public Galaxy tool sheds. Ideally, you should set the following >> configuration setting, but not setting it defaults to using the file named >> shed_tool_conf.xml for installed tools anyway. >> >> tool_config_files = tool_conf.xml,shed_tool_conf.xml >> >> The current Galaxy central repository tip is 7276:622fd4f0a437, which you >> should pull. This is the revision that the public tool sheds are using - >> they generally always run the Galaxy central tip revision. >> >> It's very possible that since you updated after 6 months of development, >> your repository has some issues. What are the results of the following >> commands? >> >> hg diff >> >> hg status >> >> hg verify >> >> hg summary >> >> >> >> On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote: >> >>> Hi Greg, >>> >>> I guess something went wrong while update, because I updated to the >>> latest changeset: >>> >>> hg tip | grep changeset >>> changeset: 7262:4fbd05095ca7 >>> >>> Can it be because I the last time I updated was at least half a year ago >>> and the toolshed integration has been implemented afterwards? So that I >>> need to configure the toolshed before I can install something form the >>> public one? >>> >>> Thanks! >>> >>> Mattias >>> >>> >>> On 06/13/2012 05:43 PM, Greg Von Kuster wrote: Hello Mattias, Did you pull from the Galaxy central repo? The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed. Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine. Thanks, Greg Von Kuster On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: > Hi, > > I just updated my local Galaxy installation to the latest version. I am > trying out the feature to add tools directly from the toolshed, but this > is not working. It results in this error: > > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', > line 144 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', > line 106 in __call__ > environ, self.app) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', > line 543 in intercept_output > app_iter = application(environ, replacement_start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', > line 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', > line 481 in install_repository > install_tool_dependencies=install_tool_dependencies ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', > line 1228 in load_repository_contents > dist_to_shed=False ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', > line 342 in create_or_update_tool_shed_repository > installed_changeset_revision=changeset_revision, > NameError: global name 'changeset_revision' is not defined > > > > And my shed_tools_conf.xml looks like this: > > > > > > > Should I put more configuration in this file? > > Any help is appreciated. > > Thanks! > > Mattias > ___ > 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/ >>> >> > __
Re: [galaxy-dev] adding tools using toolshed is not working
Hi Greg, Here is the output of the commands: hg status M run.sh M static/fastx_icons/barcode_splitter_output_example.png M static/fastx_icons/fasta_clipping_histogram_1.png M static/fastx_icons/fasta_clipping_histogram_2.png M static/fastx_icons/fastq_nucleotides_distribution_1.png M static/fastx_icons/fastq_nucleotides_distribution_2.png M static/fastx_icons/fastq_nucleotides_distribution_3.png M static/fastx_icons/fastq_nucleotides_distribution_4.png M static/fastx_icons/fastq_quality_boxplot_1.png M static/fastx_icons/fastq_quality_boxplot_2.png M static/fastx_icons/fastq_quality_boxplot_3.png M static/fastx_icons/fastx_clipper_example.png M test-data/fasta_collapser1.out M test-data/fastq_stats1.fastq M test-data/fastx_barcode_splitter1.out M test-data/fastx_clipper1a.out M tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh M tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml M tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml M tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml M tools/sr_mapping/bowtie_wrapper.xml M tools/sr_mapping/bwa_wrapper.xml ? core ? datatypes_conf.xml.bak ? jobs/pp_rjcnfq0 ? lib/galaxy/datatypes/metagenomics.py ? lib/galaxy/datatypes/registry.py.bak ? paster.log ? paster.pid ? scripts/set_metadata.py.bak ? static/fastx_icons/fastq_nucleotides_distribution_line_graph.png ? static/images/cloud.gif ? static/images/cloud_text.png ... hg verify checking changesets checking manifests crosschecking files in changesets and manifests checking files 5932 files, 7277 changesets, 28530 total revisions hg summary parent: 7276:622fd4f0a437 tip Fix bug in packing track that is a library dataset branch: default commit: 22 modified, 290 unknown update: (current) And hg diff gives a lot of output because of the custom tool configs (290 unknown files?) Does this indicate why the changeset_revision can not be determined? Thanks! On 06/15/2012 02:58 PM, Greg Von Kuster wrote: Hi Matthias, There is really nothing to configure in your Galaxy environment in order to use the public Galaxy tool sheds. Ideally, you should set the following configuration setting, but not setting it defaults to using the file named shed_tool_conf.xml for installed tools anyway. tool_config_files = tool_conf.xml,shed_tool_conf.xml The current Galaxy central repository tip is 7276:622fd4f0a437, which you should pull. This is the revision that the public tool sheds are using - they generally always run the Galaxy central tip revision. It's very possible that since you updated after 6 months of development, your repository has some issues. What are the results of the following commands? hg diff hg status hg verify hg summary On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote: Hi Greg, I guess something went wrong while update, because I updated to the latest changeset: hg tip | grep changeset changeset: 7262:4fbd05095ca7 Can it be because I the last time I updated was at least half a year ago and the toolshed integration has been implemented afterwards? So that I need to configure the toolshed before I can install something form the public one? Thanks! Mattias On 06/13/2012 05:43 PM, Greg Von Kuster wrote: Hello Mattias, Did you pull from the Galaxy central repo? The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed. Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine. Thanks, Greg Von Kuster On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: Hi, I just updated my local Galaxy installation to the latest version. I am trying out the feature to add tools directly from the toolshed, but this is not working. It results in this error: File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 481 in install_re
Re: [galaxy-dev] adding tools using toolshed is not working
Hi Matthias, There is really nothing to configure in your Galaxy environment in order to use the public Galaxy tool sheds. Ideally, you should set the following configuration setting, but not setting it defaults to using the file named shed_tool_conf.xml for installed tools anyway. tool_config_files = tool_conf.xml,shed_tool_conf.xml The current Galaxy central repository tip is 7276:622fd4f0a437, which you should pull. This is the revision that the public tool sheds are using - they generally always run the Galaxy central tip revision. It's very possible that since you updated after 6 months of development, your repository has some issues. What are the results of the following commands? hg diff hg status hg verify hg summary On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote: > Hi Greg, > > I guess something went wrong while update, because I updated to the > latest changeset: > > hg tip | grep changeset > changeset: 7262:4fbd05095ca7 > > Can it be because I the last time I updated was at least half a year ago > and the toolshed integration has been implemented afterwards? So that I > need to configure the toolshed before I can install something form the > public one? > > Thanks! > > Mattias > > > On 06/13/2012 05:43 PM, Greg Von Kuster wrote: >> Hello Mattias, >> >> Did you pull from the Galaxy central repo? The latest change set is >> 7262:4fbd05095ca7, which is what you should be running in order to use the >> tool shed. Let me know if you in fact have the latest from central - your >> line numbers in your log below look to be different from mine. >> >> Thanks, >> >> Greg Von Kuster >> >> On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: >> >>> Hi, >>> >>> I just updated my local Galaxy installation to the latest version. I am >>> trying out the feature to add tools directly from the toolshed, but this >>> is not working. It results in this error: >>> >>> File >>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', >>> line 144 in __call__ >>> app_iter = self.application(environ, sr_checker) >>> File >>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', >>> line 106 in __call__ >>> environ, self.app) >>> File >>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', >>> line 543 in intercept_output >>> app_iter = application(environ, replacement_start_response) >>> File >>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >>> line 84 in __call__ >>> return self.application(environ, start_response) >>> File >>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >>> line 633 in __call__ >>> return self.application(environ, start_response) >>> File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', >>> line 160 in __call__ >>> body = method( trans, **kwargs ) >>> File >>> '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', >>> line 184 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File >>> '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', >>> line 481 in install_repository >>> install_tool_dependencies=install_tool_dependencies ) >>> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line >>> 1228 in load_repository_contents >>> dist_to_shed=False ) >>> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line >>> 342 in create_or_update_tool_shed_repository >>> installed_changeset_revision=changeset_revision, >>> NameError: global name 'changeset_revision' is not defined >>> >>> >>> >>> And my shed_tools_conf.xml looks like this: >>> >>> >>> >>> >>> >>> >>> Should I put more configuration in this file? >>> >>> Any help is appreciated. >>> >>> Thanks! >>> >>> Mattias >>> ___ >>> 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/ > ___ 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/
Re: [galaxy-dev] adding tools using toolshed is not working
Hi Greg, I guess something went wrong while update, because I updated to the latest changeset: hg tip | grep changeset changeset: 7262:4fbd05095ca7 Can it be because I the last time I updated was at least half a year ago and the toolshed integration has been implemented afterwards? So that I need to configure the toolshed before I can install something form the public one? Thanks! Mattias On 06/13/2012 05:43 PM, Greg Von Kuster wrote: > Hello Mattias, > > Did you pull from the Galaxy central repo? The latest change set is > 7262:4fbd05095ca7, which is what you should be running in order to use the > tool shed. Let me know if you in fact have the latest from central - your > line numbers in your log below look to be different from mine. > > Thanks, > > Greg Von Kuster > > On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: > >> Hi, >> >> I just updated my local Galaxy installation to the latest version. I am >> trying out the feature to add tools directly from the toolshed, but this >> is not working. It results in this error: >> >> File >> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', >> line 144 in __call__ >>app_iter = self.application(environ, sr_checker) >> File >> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', >> line 106 in __call__ >>environ, self.app) >> File >> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', >> line 543 in intercept_output >>app_iter = application(environ, replacement_start_response) >> File >> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >>return self.application(environ, start_response) >> File >> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >>return self.application(environ, start_response) >> File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', >> line 160 in __call__ >>body = method( trans, **kwargs ) >> File >> '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', >> line 184 in decorator >>return func( self, trans, *args, **kwargs ) >> File >> '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', >> line 481 in install_repository >>install_tool_dependencies=install_tool_dependencies ) >> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line >> 1228 in load_repository_contents >>dist_to_shed=False ) >> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line >> 342 in create_or_update_tool_shed_repository >>installed_changeset_revision=changeset_revision, >> NameError: global name 'changeset_revision' is not defined >> >> >> >> And my shed_tools_conf.xml looks like this: >> >> >> >> >> >> >> Should I put more configuration in this file? >> >> Any help is appreciated. >> >> Thanks! >> >> Mattias >> ___ >> 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/ ___ 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/
Re: [galaxy-dev] adding tools using toolshed is not working
Hello Mattias, Did you pull from the Galaxy central repo? The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed. Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine. Thanks, Greg Von Kuster On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote: > Hi, > > I just updated my local Galaxy installation to the latest version. I am > trying out the feature to add tools directly from the toolshed, but this > is not working. It results in this error: > > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', > line 144 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', > line 106 in __call__ > environ, self.app) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', > line 543 in intercept_output > app_iter = application(environ, replacement_start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', > line 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', > line 481 in install_repository > install_tool_dependencies=install_tool_dependencies ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line > 1228 in load_repository_contents > dist_to_shed=False ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line > 342 in create_or_update_tool_shed_repository > installed_changeset_revision=changeset_revision, > NameError: global name 'changeset_revision' is not defined > > > > And my shed_tools_conf.xml looks like this: > > > > > > > Should I put more configuration in this file? > > Any help is appreciated. > > Thanks! > > Mattias > ___ > 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/ ___ 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/
[galaxy-dev] adding tools using toolshed is not working
Hi, I just updated my local Galaxy installation to the latest version. I am trying out the feature to add tools directly from the toolshed, but this is not working. It results in this error: File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 481 in install_repository install_tool_dependencies=install_tool_dependencies ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 1228 in load_repository_contents dist_to_shed=False ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 342 in create_or_update_tool_shed_repository installed_changeset_revision=changeset_revision, NameError: global name 'changeset_revision' is not defined And my shed_tools_conf.xml looks like this: Should I put more configuration in this file? Any help is appreciated. Thanks! Mattias ___ 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/
