Re: [galaxy-dev] Error trying to add tools from tool shed respository
Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote: Users are getting the following error when trying to add a tool from the tool shed repository on our local galaxy instance. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) The galaxy server log shows the message included below. The main error is ValueError: too many values to unpack . From a similar previous post, the resolution was to use the latest code from Galaxy central. I just ran an hg pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but we still get the same error. Any ideas? (server log) [29/Jan/2013:08:19:05 -0400] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 HTTP/1.1 500 - http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2 Error - type 'exceptions.ValueError': too many values to unpack URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill ___ 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] Error trying to add tools from tool shed respository
Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote: Users are getting the following error when trying to add a tool from the tool shed repository on our local galaxy instance. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) The galaxy server log shows the message included below. The main error is ValueError: too many values to unpack . From a similar previous post, the resolution was to use the latest code from Galaxy central. I just ran an hg pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but we still get the same error. Any ideas? (server log) [29/Jan/2013:08:19:05 -0400] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 HTTP/1.1 500 - http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2 Error - type 'exceptions.ValueError': too many values to unpack URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote: Users are getting the following error when trying to add a tool from the tool shed repository on our local galaxy instance. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) The galaxy server log shows the message included below. The main error is ValueError: too many values to unpack . From a similar previous post, the resolution was to use the latest code from Galaxy central. I just ran an hg pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but we still get the same error. Any ideas? (server log) [29/Jan/2013:08:19:05 -0400] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 HTTP/1.1 500 - http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2 Error - type 'exceptions.ValueError': too many values to unpack URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy
Re: [galaxy-dev] Error trying to add tools from tool shed respository
I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote: Users are getting the following error when trying to add a tool from the tool shed repository on our local galaxy instance. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) The galaxy server log shows the message included below. The main error is ValueError: too many values to unpack . From a similar previous post, the resolution was to use the latest code from Galaxy central. I just ran an hg pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but we still get the same error. Any ideas? (server log) [29/Jan/2013:08:19:05 -0400] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919 HTTP/1.1 500 - http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2 Error - type 'exceptions.ValueError': too many values to unpack URL: https
Re: [galaxy-dev] Error trying to add tools from tool shed respository
To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Have you made some changes to your local Galaxy code base that require merging? On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following in your Galaxy installation directory? hg heads Thanks, Greg Von Kuster On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Not that I know of. We have only edited configuration files and .loc files for various tools. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 10:07 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Have you made some changes to your local Galaxy code base that require merging? On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Perhaps these are the files that have conflicts. You'll have to get someone local that can determine the problems with your environment that are not allowing you to get clean updates to your Galaxy code. On Jan 29, 2013, at 10:11 AM, Waldron, Michael H wrote: Not that I know of. We have only edited configuration files and .loc files for various tools. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 10:07 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Have you made some changes to your local Galaxy code base that require merging? On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe. If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist. What is the result of typing the following
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary
Re: [galaxy-dev] Error trying to add tools from tool shed respository
You might try an 'hg merge --preview' to see what it actually wants to merge. One thing to note is that most of those heads displaying have been pruned and newer versions of mercurial will correctly no longer show them. -Dannon On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu wrote: Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch
Re: [galaxy-dev] Error trying to add tools from tool shed respository
It doesn't recognize the --preview option. $ hg merge --preview hg merge: option --preview not recognized hg merge [-f] [[-r] REV] Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:15 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository You might try an 'hg merge --preview' to see what it actually wants to merge. One thing to note is that most of those heads displaying have been pruned and newer versions of mercurial will correctly no longer show them. -Dannon On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu wrote: Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Oh fun. Would it be possible for you to update mercurial? It might be easier to get a handle on what's going on. Barring that, does 'hg out' show any committed changes that need to go out? -Dannon On Jan 29, 2013, at 11:24 AM, Waldron, Michael H mwald...@email.unc.edu wrote: It doesn't recognize the --preview option. $ hg merge --preview hg merge: option --preview not recognized hg merge [-f] [[-r] REV] Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:15 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository You might try an 'hg merge --preview' to see what it actually wants to merge. One thing to note is that most of those heads displaying have been pruned and newer versions of mercurial will correctly no longer show them. -Dannon On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu wrote: Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following
Re: [galaxy-dev] Error trying to add tools from tool shed respository
I'll have to look into updating mercurial. The hg out doesn't show anything to be done. $ hg out comparing with https://bitbucket.org/galaxy/galaxy-central searching for changes no changes found Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:27 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Oh fun. Would it be possible for you to update mercurial? It might be easier to get a handle on what's going on. Barring that, does 'hg out' show any committed changes that need to go out? -Dannon On Jan 29, 2013, at 11:24 AM, Waldron, Michael H mwald...@email.unc.edu wrote: It doesn't recognize the --preview option. $ hg merge --preview hg merge: option --preview not recognized hg merge [-f] [[-r] REV] Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:15 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository You might try an 'hg merge --preview' to see what it actually wants to merge. One thing to note is that most of those heads displaying have been pruned and newer versions of mercurial will correctly no longer show them. -Dannon On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu wrote: Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu wrote: Already in the email thread. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user:Dannon Baker dannonba...@me.com date:Mon Aug 13 13:23:54 2012 -0400 summary: Branch close changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user:Dannon Baker dannonba...@me.com date:Wed Apr 18 07:59:38 2012 -0400 summary: Branch close. changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user:Dannon Baker dannonba...@me.com date:Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request. changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user:Dannon Baker dannonba...@me.com date:Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user:Daniel Blankenberg d...@bx.psu.edu date:Fri Feb 03 11:15:29 2012 -0500 summary: close branch Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor [ja...@jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost. I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean? [galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge) Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running the update, then started it afterward. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now: status = kwd.get( 'status', 'done' ) Greg Von Kuster On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote: Here is the output from hg heads. [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent
Re: [galaxy-dev] Error trying to add tools from tool shed respository
On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the parent revisions: hg parents This (or these in certain cases) might not be a repository head and thus won't appear in hg heads. If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a @ symbol) in the code history: hg glog | more If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with: hg clone . ../galaxy-dist-test Then, you'd move into this clone: cd ../galaxy-dist-test You might need to update to the version previously printed by hg parents above: hg update revision One might then assume that any desirable update would involve getting to the tip, and so you could try a merge with that: hg merge tip If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed: hg commit Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong. Doing this might be quicker than having to get a more recent Mercurial version installed. Paul ___ 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] Error trying to add tools from tool shed respository
Forgot to also include the hg parents output. $ hg parents changeset: 7986:12fcd068b12e user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads) [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Paul Boddie [paul.bod...@biotek.uio.no] Sent: Tuesday, January 29, 2013 12:01 PM To: James Taylor Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the parent revisions: hg parents This (or these in certain cases) might not be a repository head and thus won't appear in hg heads. If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a @ symbol) in the code history: hg glog | more If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with: hg clone . ../galaxy-dist-test Then, you'd move into this clone: cd ../galaxy-dist-test You might need to update to the version previously printed by hg parents above: hg update revision One might then assume that any desirable update would involve getting to the tip, and so you could try a merge with that: hg merge tip If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed: hg commit Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong. Doing this might be quicker than having to get a more recent Mercurial version installed. Paul ___ 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] Error trying to add tools from tool shed respository
So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened. Anyway, at this point, does `hg update --check` actually work? And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape. On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Forgot to also include the hg parents output. $ hg parents changeset: 7986:12fcd068b12e user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads) [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Paul Boddie [paul.bod...@biotek.uio.no] Sent: Tuesday, January 29, 2013 12:01 PM To: James Taylor Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the parent revisions: hg parents This (or these in certain cases) might not be a repository head and thus won't appear in hg heads. If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a @ symbol) in the code history: hg glog | more If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with: hg clone . ../galaxy-dist-test Then, you'd move into this clone: cd ../galaxy-dist-test You might need to update to the version previously printed by hg parents above: hg update revision One might then assume that any desirable update would involve getting to the tip, and so you could try a merge with that: hg merge tip If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed: hg commit Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong. Doing this might be quicker than having to get a more recent Mercurial version installed. Paul ___ 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] Error trying to add tools from tool shed respository
The hg update --check command reports the following: $ hg update --check abort: uncommitted local changes I just connected to the #galaxyproject IRC channel. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened. Anyway, at this point, does `hg update --check` actually work? And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape. On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Forgot to also include the hg parents output. $ hg parents changeset: 7986:12fcd068b12e user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads) [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Paul Boddie [paul.bod...@biotek.uio.no] Sent: Tuesday, January 29, 2013 12:01 PM To: James Taylor Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the parent revisions: hg parents This (or these in certain cases) might not be a repository head and thus won't appear in hg heads. If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a @ symbol) in the code history: hg glog | more If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with: hg clone . ../galaxy-dist-test Then, you'd move into this clone: cd ../galaxy-dist-test You might need to update to the version previously printed by hg parents above: hg update revision One might then assume that any desirable update would involve getting to the tip, and so you could try a merge with that: hg merge tip If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed: hg commit Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong. Doing this might be quicker than having to get a more recent Mercurial version installed. Paul ___ 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
Re: [galaxy-dev] Error trying to add tools from tool shed respository
I don't know why I thought we'd already checked this, but -- 'hg st' will tell you which files have been modified in your local repository, and 'hg diff' will tell you exactly what changes have taken place I'm not sure of the exact state of your repository at the moment, so this *might* display all changes from the pull as well, which wouldn't be particularly useful. Worth trying, though. Don't see you in #galaxyproject yet, sure it's working? On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu wrote: The hg update --check command reports the following: $ hg update --check abort: uncommitted local changes I just connected to the #galaxyproject IRC channel. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened. Anyway, at this point, does `hg update --check` actually work? And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape. On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Forgot to also include the hg parents output. $ hg parents changeset: 7986:12fcd068b12e user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads) [galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user:jeremy goecks jeremy.goe...@emory.edu date:Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Paul Boddie [paul.bod...@biotek.uio.no] Sent: Tuesday, January 29, 2013 12:01 PM To: James Taylor Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which version of the Galaxy code you're using now as defined by the parent revisions: hg parents This (or these in certain cases) might not be a repository head and thus won't appear in hg heads. If you have the graphlog extension enabled, running the following might be informative as it should show you where you are (with a @ symbol) in the code history: hg glog | more If you don't want to risk your working directory, you could first clone it to make something that you can then experiment with: hg clone . ../galaxy-dist-test Then, you'd move into this clone: cd ../galaxy-dist-test You might need to update to the version previously printed by hg parents above: hg update revision One might then assume that any desirable update would involve getting to the tip, and so you could try a merge with that: hg merge tip If all of this works reasonably, you should be able to do the same merge on your real working directory (and can thus delete the test directory). The result of any merge will need to be committed: hg commit Anyway, these are just some thoughts. The crucial point is that you can clone the repository and then work with the clone, discarding it if your experiments go wrong
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Here is hg st output: $ hg st M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_datasets_main.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/delete_userless_histories_main.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_datasets_main.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_folders_main.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_histories_main.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/cleanup_datasets/purge_libraries_main.sh M scripts/cleanup_datasets/update_metadata.sh M tools/peak_calling/macs_wrapper.xml M tools/plotting/boxplot.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/bowtie2_wrapper.xml M tools/sr_mapping/bowtie_color_wrapper.xml M tools/sr_mapping/bowtie_wrapper.xml M tools/sr_mapping/bwa_color_wrapper.xml M tools/sr_mapping/bwa_wrapper.xml ? contrib/galaxy-init ? galaxy_cleanup.log ? galaxy_cleanup.sh ? migrated_tools_conf.xml.110712 ? paster.pid ? scripts/cleanup_datasets/delete_userless_histories.log ? scripts/cleanup_datasets/purge_datasets.log ? scripts/cleanup_datasets/purge_folders.log ? scripts/cleanup_datasets/purge_histories.log ? scripts/cleanup_datasets/purge_libraries.log ? static/UNC_galaxy_mirror_housekeeping_notes.pdf ? tool-data/bwa_index.loc.sample ? tool-data/bwa_index_color.loc.sample ? tool-data/tool_data_table_conf.xml.sample ? tool_conf.xml.110212 ? tool_conf.xml.new ? tool_data_table_conf.xml.030112 ? tools/plotting/boxplot.xml.012512 ? typescript The hg diff output is quite long. It turns out I didn't connect to the IRC channel. I have XChat IRC client, but not familiar with using it. How to I connect to the irc.freenode.net server to access the #galaxyproject channel? Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:48 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository I don't know why I thought we'd already checked this, but -- 'hg st' will tell you which files have been modified in your local repository, and 'hg diff' will tell you exactly what changes have taken place I'm not sure of the exact state of your repository at the moment, so this *might* display all changes from the pull as well, which wouldn't be particularly useful. Worth trying, though. Don't see you in #galaxyproject yet, sure it's working? On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu wrote: The hg update --check command reports the following: $ hg update --check abort: uncommitted local changes I just connected to the #galaxyproject IRC channel. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened. Anyway, at this point, does `hg update --check` actually work? And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape. On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Forgot to also include the hg parents output. $ hg parents changeset: 7986:12fcd068b12e user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Waldron, Michael H Sent: Tuesday, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev
Re: [galaxy-dev] Error trying to add tools from tool shed respository
Ok, so that confirms that you definitely have local customizations we'll want to make sure to keep. What I'd do before we go any further is this: `hg diff -p local_changes.patch` This will save all of your current changes to a patch, should we have to recreate them (though I don't expect this). `hg ci -m Local changes to cleanup_datasets and various tools` Which will commit your local changes to your local repository. At this point, hopefully, you can just 'hg update', possibly needing to merge as well. For IRC: Just join the Freenode network shown in XChat, and then Join Channel should pop up a box you can put #galaxyproject in On Jan 29, 2013, at 1:52 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Here is hg st output: $ hg st M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_datasets_main.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/delete_userless_histories_main.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_datasets_main.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_folders_main.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_histories_main.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/cleanup_datasets/purge_libraries_main.sh M scripts/cleanup_datasets/update_metadata.sh M tools/peak_calling/macs_wrapper.xml M tools/plotting/boxplot.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/bowtie2_wrapper.xml M tools/sr_mapping/bowtie_color_wrapper.xml M tools/sr_mapping/bowtie_wrapper.xml M tools/sr_mapping/bwa_color_wrapper.xml M tools/sr_mapping/bwa_wrapper.xml ? contrib/galaxy-init ? galaxy_cleanup.log ? galaxy_cleanup.sh ? migrated_tools_conf.xml.110712 ? paster.pid ? scripts/cleanup_datasets/delete_userless_histories.log ? scripts/cleanup_datasets/purge_datasets.log ? scripts/cleanup_datasets/purge_folders.log ? scripts/cleanup_datasets/purge_histories.log ? scripts/cleanup_datasets/purge_libraries.log ? static/UNC_galaxy_mirror_housekeeping_notes.pdf ? tool-data/bwa_index.loc.sample ? tool-data/bwa_index_color.loc.sample ? tool-data/tool_data_table_conf.xml.sample ? tool_conf.xml.110212 ? tool_conf.xml.new ? tool_data_table_conf.xml.030112 ? tools/plotting/boxplot.xml.012512 ? typescript The hg diff output is quite long. It turns out I didn't connect to the IRC channel. I have XChat IRC client, but not familiar with using it. How to I connect to the irc.freenode.net server to access the #galaxyproject channel? Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:48 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository I don't know why I thought we'd already checked this, but -- 'hg st' will tell you which files have been modified in your local repository, and 'hg diff' will tell you exactly what changes have taken place I'm not sure of the exact state of your repository at the moment, so this *might* display all changes from the pull as well, which wouldn't be particularly useful. Worth trying, though. Don't see you in #galaxyproject yet, sure it's working? On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu wrote: The hg update --check command reports the following: $ hg update --check abort: uncommitted local changes I just connected to the #galaxyproject IRC channel. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best guess was that this was caused by swapping from galaxy-dist to galaxy-central in the situation where galaxy-dist has had changesets applied directly and then ported to galaxy-central out of order, combined with your oder version of mercurial. That parent, however, would have been before that happened. Anyway, at this point, does `hg update --check` actually work? And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be faster to iterate through what we need to do to get your repository back in shape. On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Forgot to also include the hg parents output. $ hg parents
Re: [galaxy-dev] Error trying to add tools from tool shed respository
With Dannon's help, I was able to straighten out our local installation by doing the following: Update mercurial to new version (2.4.2) for hg to work as expected. Commit local changes: hg diff -p local_changes.patch (save local changes as a patch, in case needed) hg ci -m Local changes to cleanup_datasets and various tools (commit changes) hg update (no files unresolved) hg tip (shows latest update) hg heads (shows 2 heads so need to merge) hg merge hg ci -m Merged changes (commit merged changes) hg head (only 1 head now) Restarted server, ran the needed database migration script and option tool migration script. The instance is now successfully updated, and this fixed the original problem of not being able to install a tool from the tool shed. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 2:04 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Ok, so that confirms that you definitely have local customizations we'll want to make sure to keep. What I'd do before we go any further is this: `hg diff -p local_changes.patch` This will save all of your current changes to a patch, should we have to recreate them (though I don't expect this). `hg ci -m Local changes to cleanup_datasets and various tools` Which will commit your local changes to your local repository. At this point, hopefully, you can just 'hg update', possibly needing to merge as well. For IRC: Just join the Freenode network shown in XChat, and then Join Channel should pop up a box you can put #galaxyproject in On Jan 29, 2013, at 1:52 PM, Waldron, Michael H mwald...@email.unc.edu wrote: Here is hg st output: $ hg st M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_datasets_main.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/delete_userless_histories_main.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_datasets_main.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_folders_main.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_histories_main.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/cleanup_datasets/purge_libraries_main.sh M scripts/cleanup_datasets/update_metadata.sh M tools/peak_calling/macs_wrapper.xml M tools/plotting/boxplot.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/bowtie2_wrapper.xml M tools/sr_mapping/bowtie_color_wrapper.xml M tools/sr_mapping/bowtie_wrapper.xml M tools/sr_mapping/bwa_color_wrapper.xml M tools/sr_mapping/bwa_wrapper.xml ? contrib/galaxy-init ? galaxy_cleanup.log ? galaxy_cleanup.sh ? migrated_tools_conf.xml.110712 ? paster.pid ? scripts/cleanup_datasets/delete_userless_histories.log ? scripts/cleanup_datasets/purge_datasets.log ? scripts/cleanup_datasets/purge_folders.log ? scripts/cleanup_datasets/purge_histories.log ? scripts/cleanup_datasets/purge_libraries.log ? static/UNC_galaxy_mirror_housekeeping_notes.pdf ? tool-data/bwa_index.loc.sample ? tool-data/bwa_index_color.loc.sample ? tool-data/tool_data_table_conf.xml.sample ? tool_conf.xml.110212 ? tool_conf.xml.new ? tool_data_table_conf.xml.030112 ? tools/plotting/boxplot.xml.012512 ? typescript The hg diff output is quite long. It turns out I didn't connect to the IRC channel. I have XChat IRC client, but not familiar with using it. How to I connect to the irc.freenode.net server to access the #galaxyproject channel? Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:48 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository I don't know why I thought we'd already checked this, but -- 'hg st' will tell you which files have been modified in your local repository, and 'hg diff' will tell you exactly what changes have taken place I'm not sure of the exact state of your repository at the moment, so this *might* display all changes from the pull as well, which wouldn't be particularly useful. Worth trying, though. Don't see you in #galaxyproject yet, sure it's working? On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu wrote: The hg update --check command reports the following: $ hg update --check abort: uncommitted local changes I just connected to the #galaxyproject IRC channel. Mike Waldron Systems Specialist ITS
