Re: [galaxy-dev] shed_tool_conf.xml not updated
Hello Anne, I apologize for the delay in responding to you on this. The first issue I see is that the revision of your local Galaxy instance implies that your repo is not being updated from the Galaxy central repository on bitbucket. Unfortunately in order to use the tool shed, you local Galaxy instance must be up to date with the central repository since the Galaxy distribution repository generally lags 6 to 8 weeks behind the central repository, and so the communication between Galaxy and the tool shed is often not functionally correct. The central repository on bitbucket is current at revision 6626:d8af2f7b1f35. For clarification what value have you set for the tool_path config setting in your shed_tool_conf.xml file? After you update your Galaxy instance, try installing the tool again and let me know if you encounter issues. Thanks very much! Greg Von Kuster On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: Hello, When installing a tool from the tool shed repository into our local instance, I've got a page with Server error. When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. Bellow is my previous email server error when installing tool from tool shed repository into local instance sent two days ago detailing what I have done and the log related to the error. Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. Let me know if you have any suggestions. Kind regards, Anne. On 25 Jan 2012, at 16:43, Anne Pajon wrote: Hello, I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) without success. Here is what I've done. (1) I've edited my universe_wsgi.ini # -- Files and directories # Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. tool_config_file = tool_conf.xml,shed_tool_conf.xml # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the toolbox tag. tool_path = tools (2) I've created the directory shed_tools/ above the galaxy-dist/ as recommended (3) I've restarted the server (4) I've logged in as admin user. I've clicked the Admin link in the top Galaxy tool panel to display the Galaxy Administration interface and then Search and browse tool sheds under Tool sheds from the left blue section to display the Accessible Galaxy tool sheds page, click Galaxy main tool shed to display the valid repositories and choose tabular2html and click on Install to local Galaxy, select the panel section and click Install. I get a page with Server Error. Strangely, the tool appears in the list of tools and works in my Galaxy instance. The tool files have been installed on disk at the directory created in (2) but the shed_tool_conf.xml has not been updated. After restarting my Galaxy server, the tool is not visible anymore. Here is what appears in the log related to the installation of the tool: galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Installing repository 'tabular2html' galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html galaxy.util.shed_util DEBUG 2012-01-25 14:20:55,486 Updating cloned repository to revision a5814dd5a11a galaxy.tools DEBUG 2012-01-25 14:20:55,652 Reloading section: My Tools galaxy.tools DEBUG 2012-01-25 14:20:55,673 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0 .0. 143.65.172.178 - - [25/Jan/2012:14:20:54 +0100] POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.ps u.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c6573 2066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f74616275 6c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/insta ll_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d 6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hello Greg, Thanks a lot for your answer and sorry for having sent two emails. Regarding the version of our local instance, I understand perfectly that the Galaxy distribution repository is behind the Galaxy central repository but we would like to use Galaxy on a production server and we are looking at stable releases not development ones. What would you advice us to do? Here is the value for tool_path in my shed_tool_conf.xml: ?xml version=1.0? toolbox tool_path=../shed_tools /toolbox I'm waiting your advice to migrate my repository from Galaxy distribution to Galaxy central. Thanks in advance. Kind regards, Anne. On 27 Jan 2012, at 13:03, Greg Von Kuster wrote: Hello Anne, I apologize for the delay in responding to you on this. The first issue I see is that the revision of your local Galaxy instance implies that your repo is not being updated from the Galaxy central repository on bitbucket. Unfortunately in order to use the tool shed, you local Galaxy instance must be up to date with the central repository since the Galaxy distribution repository generally lags 6 to 8 weeks behind the central repository, and so the communication between Galaxy and the tool shed is often not functionally correct. The central repository on bitbucket is current at revision 6626:d8af2f7b1f35. For clarification what value have you set for the tool_path config setting in your shed_tool_conf.xml file? After you update your Galaxy instance, try installing the tool again and let me know if you encounter issues. Thanks very much! Greg Von Kuster On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: Hello, When installing a tool from the tool shed repository into our local instance, I've got a page with Server error. When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. Bellow is my previous email server error when installing tool from tool shed repository into local instance sent two days ago detailing what I have done and the log related to the error. Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. Let me know if you have any suggestions. Kind regards, Anne. On 25 Jan 2012, at 16:43, Anne Pajon wrote: Hello, I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) without success. Here is what I've done. (1) I've edited my universe_wsgi.ini # -- Files and directories # Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. tool_config_file = tool_conf.xml,shed_tool_conf.xml # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the toolbox tag. tool_path = tools (2) I've created the directory shed_tools/ above the galaxy-dist/ as recommended (3) I've restarted the server (4) I've logged in as admin user. I've clicked the Admin link in the top Galaxy tool panel to display the Galaxy Administration interface and then Search and browse tool sheds under Tool sheds from the left blue section to display the Accessible Galaxy tool sheds page, click Galaxy main tool shed to display the valid repositories and choose tabular2html and click on Install to local Galaxy, select the panel section and click Install. I get a page with Server Error. Strangely, the tool appears in the list of tools and works in my Galaxy instance. The tool files have been installed on disk at the directory created in (2) but the shed_tool_conf.xml has not been updated. After restarting my Galaxy server, the tool is not visible anymore. Here is what appears in the log related to the installation of the tool: galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Installing repository 'tabular2html' galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html galaxy.util.shed_util DEBUG 2012-01-25 14:20:55,486 Updating cloned repository to revision a5814dd5a11a galaxy.tools DEBUG 2012-01-25 14:20:55,652 Reloading section: My Tools galaxy.tools DEBUG 2012-01-25 14:20:55,673 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0 .0. 143.65.172.178 - - [25/Jan/2012:14:20:54 +0100] POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.ps
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Anne, A new update to the Galaxy distribution repository is planned for today, I believe, so unless that changes you should be able to update your Galaxy instance either today or Monday using the distribution repository. However, this problem will continue to exist between Galaxy instances that track the distribution repository and that also want to take advantage of the Galaxy tool shed features that enable direct interaction between Galaxy and the tool shed. The tool shed features are implement much more rapidly than the Galaxy distribution is updated, resulting in this ongoing problem. Regarding the state of your local instance and the tool shed repository you attempted to install - if I understand correctly, the repository was successfully installed on disk, but the XML tag set entry for the contained tool was not added to your shed_tool_conf.xml file. If this is the case, then you'll need to manually remove the installed tool shed repository from disk before you try installing it again after updating your Galaxy instance to the new upcoming distribution. Sorry for the inconvenience. Greg On Jan 27, 2012, at 9:35 AM, Anne Pajon wrote: Hello Greg, Thanks a lot for your answer and sorry for having sent two emails. Regarding the version of our local instance, I understand perfectly that the Galaxy distribution repository is behind the Galaxy central repository but we would like to use Galaxy on a production server and we are looking at stable releases not development ones. What would you advice us to do? Here is the value for tool_path in my shed_tool_conf.xml: ?xml version=1.0? toolbox tool_path=../shed_tools /toolbox I'm waiting your advice to migrate my repository from Galaxy distribution to Galaxy central. Thanks in advance. Kind regards, Anne. On 27 Jan 2012, at 13:03, Greg Von Kuster wrote: Hello Anne, I apologize for the delay in responding to you on this. The first issue I see is that the revision of your local Galaxy instance implies that your repo is not being updated from the Galaxy central repository on bitbucket. Unfortunately in order to use the tool shed, you local Galaxy instance must be up to date with the central repository since the Galaxy distribution repository generally lags 6 to 8 weeks behind the central repository, and so the communication between Galaxy and the tool shed is often not functionally correct. The central repository on bitbucket is current at revision 6626:d8af2f7b1f35. For clarification what value have you set for the tool_path config setting in your shed_tool_conf.xml file? After you update your Galaxy instance, try installing the tool again and let me know if you encounter issues. Thanks very much! Greg Von Kuster On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: Hello, When installing a tool from the tool shed repository into our local instance, I've got a page with Server error. When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. Bellow is my previous email server error when installing tool from tool shed repository into local instance sent two days ago detailing what I have done and the log related to the error. Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. Let me know if you have any suggestions. Kind regards, Anne. On 25 Jan 2012, at 16:43, Anne Pajon wrote: Hello, I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) without success. Here is what I've done. (1) I've edited my universe_wsgi.ini # -- Files and directories # Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. tool_config_file = tool_conf.xml,shed_tool_conf.xml # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the toolbox tag. tool_path = tools (2) I've created the directory shed_tools/ above the galaxy-dist/ as recommended (3) I've restarted the server (4) I've logged in as admin user. I've clicked the Admin link in the top Galaxy tool panel to display the Galaxy Administration interface and then Search and browse tool sheds under Tool sheds from the left blue section to display the Accessible Galaxy tool sheds page, click Galaxy main tool shed to display the valid repositories and choose tabular2html
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Greg, Thanks a lot. I have the impression from what I read on the wiki that Galaxy will be using the tool shed to provide more flexibility in choosing tools instead of having them bundle in the current distribution. We are very much interested by these new features because we only use a subset of the available tools plus some that we have developed in house. From what you are saying, I have the impression that I will be better of running my Galaxy instance against the central repository instead of the distribution one if I do not want to wait for bug fixes. Am I right of thinking that? If so, I will migrate to the central repository and let you know how it goes. Before migrating and updating I will manually remove the installed tool shed repository from disk as you advised. Kind regards, Anne. On 27 Jan 2012, at 14:57, Greg Von Kuster wrote: Hi Anne, A new update to the Galaxy distribution repository is planned for today, I believe, so unless that changes you should be able to update your Galaxy instance either today or Monday using the distribution repository. However, this problem will continue to exist between Galaxy instances that track the distribution repository and that also want to take advantage of the Galaxy tool shed features that enable direct interaction between Galaxy and the tool shed. The tool shed features are implement much more rapidly than the Galaxy distribution is updated, resulting in this ongoing problem. Regarding the state of your local instance and the tool shed repository you attempted to install - if I understand correctly, the repository was successfully installed on disk, but the XML tag set entry for the contained tool was not added to your shed_tool_conf.xml file. If this is the case, then you'll need to manually remove the installed tool shed repository from disk before you try installing it again after updating your Galaxy instance to the new upcoming distribution. Sorry for the inconvenience. Greg On Jan 27, 2012, at 9:35 AM, Anne Pajon wrote: Hello Greg, Thanks a lot for your answer and sorry for having sent two emails. Regarding the version of our local instance, I understand perfectly that the Galaxy distribution repository is behind the Galaxy central repository but we would like to use Galaxy on a production server and we are looking at stable releases not development ones. What would you advice us to do? Here is the value for tool_path in my shed_tool_conf.xml: ?xml version=1.0? toolbox tool_path=../shed_tools /toolbox I'm waiting your advice to migrate my repository from Galaxy distribution to Galaxy central. Thanks in advance. Kind regards, Anne. On 27 Jan 2012, at 13:03, Greg Von Kuster wrote: Hello Anne, I apologize for the delay in responding to you on this. The first issue I see is that the revision of your local Galaxy instance implies that your repo is not being updated from the Galaxy central repository on bitbucket. Unfortunately in order to use the tool shed, you local Galaxy instance must be up to date with the central repository since the Galaxy distribution repository generally lags 6 to 8 weeks behind the central repository, and so the communication between Galaxy and the tool shed is often not functionally correct. The central repository on bitbucket is current at revision 6626:d8af2f7b1f35. For clarification what value have you set for the tool_path config setting in your shed_tool_conf.xml file? After you update your Galaxy instance, try installing the tool again and let me know if you encounter issues. Thanks very much! Greg Von Kuster On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: Hello, When installing a tool from the tool shed repository into our local instance, I've got a page with Server error. When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. Bellow is my previous email server error when installing tool from tool shed repository into local instance sent two days ago detailing what I have done and the log related to the error. Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. Let me know if you have any suggestions. Kind regards, Anne. On 25 Jan 2012, at 16:43, Anne Pajon wrote: Hello, I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) without success. Here is what I've done. (1) I've edited my universe_wsgi.ini # -- Files and directories # Tool
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Greg, Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 from Galaxy central repository. I tried again to install tabular2html from the tool shed, but I get the same problem (Server Error when installing and shed_tool_conf.xml not updated). Here is my log in case it helps. galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Installing repository 'tabular2html' galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,839 Updating cloned repository to revision a5814dd5a11a galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,982 Adding new row (or updating an existing row) for repository 'tabular2html' in the tool_shed_repository table. galaxy.tools DEBUG 2012-01-27 19:20:54,050 Reloading section: My Tools galaxy.tools DEBUG 2012-01-27 19:20:54,078 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0.0. 143.65.172.178 - - [27/Jan/2012:19:20:52 +0100] POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True; Mozilla/5.0 (Macintosh! ; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 Error - type 'exceptions.TypeError': cannot serialize None (type NoneType) URL: http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 284 in install_repository dist_to_shed=False ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 649 in load_repository_contents uninstall=False ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 782 in alter_tool_panel config_elems_to_xml_file( app, shed_tool_conf_dict ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 25 in config_elems_to_xml_file os.write( fd, '%s' % util.xml_to_string( elem, pretty=True ) ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/__init__.py', line 113 in xml_to_string return ElementTree.tostring( pretty_print_xml( elem ) ) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 1006 in tostring File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 660 in write File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 695 in _write File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 827 in _escape_attrib File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 774 in _raise_serialization_error TypeError: cannot serialize None (type
[galaxy-dev] Tophat Error?
Hi everyone, I have a *.qual file and I ran Tophat on the public galaxy server but I got the following error. I am wondering if anyone has a solution for this. Thank you Input: QUAL Groomer file Database: hg19 Full Error: Error in tophat: [Tue Jan 17 10:55:08 2012] Beginning TopHat run (v1.4.0) --- [Tue Jan 17 10:55:08 2012] Preparing output location ./tophat_out/ [Tue Jan 17 10:55:08 2012] Checking for Bowtie index files [Tue Jan 17 10:55:08 2012] Checking for reference FASTA file [Tue Jan 17 10:55:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Jan 17 10:55:08 2012] Checking for Samtools Samtools Version: 0.1.12 [Tue Jan 17 10:55:08 2012] Generating SAM header for /galaxy/data/hg19/hg19full/bowtie_index/hg19full format: fastq quality scale: phred33 (default) [Tue Jan 17 10:55:34 2012] Preparing reads left reads: min. length=50, count=5247 [Tue Jan 17 10:55:34 2012] Mapping left_kept_reads against hg19full with Bowtie [Tue Jan 17 10:55:36 2012] Processing bowtie hits [Tue Jan 17 10:57:03 2012] Mapping left_kept_reads_seg1 against hg19full with Bowtie (1/21) [Tue Jan 17 10:57:04 2012] Mapping left_kept_reads_seg2 against hg19full with Bowtie (2/21) [Tue Jan 17 10:57:05 2012] Mapping left_kept_reads_seg3 against hg19full with Bowtie (3/21) [Tue Jan 17 10:57:07 2012] Mapping left_kept_reads_seg4 against hg19full with Bowtie (4/21) [Tue Jan 17 10:57:08 2012] Mapping left_kept_reads_seg5 against hg19full with Bowtie (5/21) [Tue Jan 17 10:57:10 2012] Mapping left_kept_reads_seg6 against hg19full with Bowtie (6/21) [Tue Jan 17 10:57:11 2012] Mapping left_kept_reads_seg7 against hg19full with Bowtie (7/21) [Tue Jan 17 10:57:12 2012] Mapping left_kept_reads_seg8 against hg19full with Bowtie (8/21) [Tue Jan 17 10:57:13 2012] Mapping left_kept_reads_seg9 against hg19full with Bowtie (9/21) [Tue Jan 17 10:57:15 2012] Mapping left_kept_reads_seg10 against hg19full with Bowtie (10/21) [Tue Jan 17 10:57:16 2012] Mapping left_kept_reads_seg11 against hg19full with Bowtie (11/21) [Tue Jan 17 10:57:17 2012] Mapping left_kept_reads_seg12 against hg19full with Bowtie (12/21) [Tue Jan 17 10:57:18 2012] Mapping left_kept_reads_seg13 against hg19full with Bowtie (13/21) [Tue Jan 17 10:57:19 2012] Mapping left_kept_reads_seg14 against hg19full with Bowtie (14/21) [Tue Jan 17 10:57:20 2012] Mapping left_kept_reads_seg15 against hg19full with Bowtie (15/21) [Tue Jan 17 10:57:21 2012] Mapping left_kept_reads_seg16 against hg19full with Bowtie (16/21) [Tue Jan 17 10:57:22 2012] Mapping left_kept_reads_seg17 against hg19full with Bowtie (17/21) [Tue Jan 17 10:57:23 2012] Mapping left_kept_reads_seg18 against hg19full with Bowtie (18/21) [Tue Jan 17 10:57:24 2012] Mapping left_kept_reads_seg19 against hg19full with Bowtie (19/21) [Tue Jan 17 10:57:25 2012] Mapping left_kept_reads_seg20 against hg19full with Bowtie (20/21) [Tue Jan 17 10:57:26 2012] Mapping left_kept_reads_seg21 against hg19full with Bowtie (21/21) [Tue Jan 17 10:57:27 2012] Searching for junctions via segment mapping [Tue Jan 17 10:58:42 2012] Retrieving sequences for splices [Tue Jan 17 11:02:24 2012] Indexing splices [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg3 against segment_juncs with Bowtie (3/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg4 against segment_juncs with Bowtie (4/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg5 against segment_juncs with Bowtie (5/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg6 against segment_juncs with Bowtie (6/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg7 against segment_juncs with Bowtie (7/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg8 against segment_juncs with Bowtie (8/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg9 against segment_juncs with Bowtie (9/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg10 against segment_juncs with Bowtie (10/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg11 against segment_juncs with Bowtie (11/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg12 against segment_juncs with Bowtie (12/21) [Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg13 against segment_juncs with Bowtie (13/21) [Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg14 against segment_juncs with Bowtie (14/21) [Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg15 against segment_juncs with Bowtie (15/21) [Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg16 against segment_juncs with Bowtie (16/21) [Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg17 against segment_juncs with Bowtie (17/21) [Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg18 against segment_juncs with Bowtie
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Anne, OK, the only other thing this could be is that the metadata column in the tool_shed_repository database table for this repository got corrupted during the initial install when the revision of your Galaxy instance was not up to date. So, if the repository once again got installed on disk, but the entry for the tool didn't make it into shed_tool_conf,xml, then manually remove the repository from disk again. Then either update the metadata column in the tool shed repository table for this repository to be null or delete the record from the table. If you're using postgres, then the update statement would be something like: update tool_shed_repository set metadata = null where id = whatever the id is of the tabular2html tool shed repository You could also delete this record from the table and it will be recreated when you install the repository. After taking these 2 steps, you should be able to install the tool with no problem. However, if there is an entry in your shed_tool_conf.xml file, remove it manually before attempting to reinstall. Sorry for all of this, but once you have your environment cleared up (following the steps above) and you're running the correct change set, installing from the tool shed should not cause you problems. Let me know how this goes. Greg Von Kuster On Jan 27, 2012, at 2:27 PM, Anne Pajon wrote: Hi Greg, Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 from Galaxy central repository. I tried again to install tabular2html from the tool shed, but I get the same problem (Server Error when installing and shed_tool_conf.xml not updated). Here is my log in case it helps. galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Installing repository 'tabular2html' galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,839 Updating cloned repository to revision a5814dd5a11a galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,982 Adding new row (or updating an existing row) for repository 'tabular2html' in the tool_shed_repository table. galaxy.tools DEBUG 2012-01-27 19:20:54,050 Reloading section: My Tools galaxy.tools DEBUG 2012-01-27 19:20:54,078 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0.0. 143.65.172.178 - - [27/Jan/2012:19:20:52 +0100] POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True; Mozilla/5.0 (Macinto! sh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 Error - type 'exceptions.TypeError': cannot serialize None (type NoneType) URL: http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 284 in install_repository dist_to_shed=False
[galaxy-dev] Error executing tool: 'fasta'
Hi, I have tried running (on my local instance) a number of tools (fasta_to_tabular, tandem_repeat_finder, others) on my fasta file but keep getting the error Error executing tool: 'fasta' after file execution. In the log file I see this 10.1.1.119 - - [27/Jan/2012:15:47:15 -0400] GET /tool_runner?tool_id=fasta2tab HTTP/1.1 200 - http://domain:8080/root/tool_menu; Mozilla/5.0 (Windows NT 5.2; WOW64; rv:6.0) Gecko/20100101 Firefox/6.0 galaxy.tools ERROR 2012-01-27 15:47:17,647 Exception caught while attempting tool execution: Traceback (most recent call last): File /Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py, line 1184, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File /Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py, line 1503, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File /Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py, line 199, in execute build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) KeyError: 'fasta' The fasta file is ok because I have a development installation and the tools work fine there. So there is something wrong with my production installation. I did a diff between the files galaxy_dist/lib/galaxy/tools/__init__.py and lib/galaxy/tools/actions/__init__.py but they are the same. Any help would be much appreciated. Thanks, Liisa___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)
Hi All, We are finally up-and-running again with the latest dist release. The previoous version was ok but already quite old. For our local public server at wur we are now encountering the awaited disk space issues. as had to come some daybut sooner anyway... So we have been cleaning up. Used the cleanusp scripts for marked as deleted files and such. But two issues remain for galaxy-admin users: 1) How to really delete a user and its non (no-longer) shared files? (from the admin panel) 2) Is there a way to get the user disk space usage in the admin panel (or using some other method?)? Thereby we can contact that user to push cleaning up files. Thanks Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] January 27, 2012 Galaxy Distribution News Brief
January 27, 2012 Galaxy Distribution News Brief Complete News Brief * http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27 Highlights: * Important metadata and Python 2.5 support corrections * SAMtools upgraded for version 0.1.18. Mpileup added. * Dynamic filtering, easy color options, and quicker indexing enhance Trackster * Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner * Improvements to metadata handling and searching in the Tool Shed * Improved solutions for schema access, jobs management, workflow imports and inputs. * New datatypes (Eland, XML), multiple tool enhancements, and bug fixes. Get Galaxy! * http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 26920e20157f Read the release announcement and see the prior release history * http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Need help with a local instance? Search with our custom google tools! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching And consider subscribing to the galaxy-dev mailing list! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing -- Jennifer Jackson Galaxy Team http://usegalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki/Support ___ 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/
