Hi, Just wanted to let you know that my tophat2 install is working now. In case it helps someone else in the future: Manually placing tool_dependencies.xml in the correct shed_tools directory, placing the tool dependency package in the correct dependencies directory, and uninstalling and then installing the tool dependency package worked.
Thanks for the advice. -Sheldon -----Original Message----- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Tuesday, March 25, 2014 10:34 AM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] tophat2 install If you installe dit from the main Tool Shed, then this repository has the recipe for installing the package. http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 Greg Von Kuster On Mar 25, 2014, at 9:25 AM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> wrote: > Hi, > > Not sure if you saw my last email. Updating to the latest patch version > doesn't seem to help. I was wondering where I could get the galaxy package > version of tophat2 and put it where it needs to be manually. Then I could > try the uninstall/install and see if that helps. > > Thanks! > -Sheldon > > -----Original Message----- > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, > Sheldon > Sent: Thursday, March 20, 2014 3:11 PM > To: 'Greg Von Kuster' > Cc: galaxy-dev@lists.bx.psu.edu Dev > Subject: Re: [galaxy-dev] tophat2 install > > No difference. Same error > > -----Original Message----- > From: Greg Von Kuster [mailto:g...@bx.psu.edu] > Sent: Thursday, March 20, 2014 2:56 PM > To: Briand, Sheldon > Cc: galaxy-dev@lists.bx.psu.edu Dev > Subject: Re: [galaxy-dev] tophat2 install > > Sorry, should have advised this: > >> hg pull https://bitbucket.org/galaxy/galaxy-central#stable >> hg update stable > > See the end ot this thread: > > http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-eve > n-after-canceling-job-in-galaxy-td4663719.html > > > > > On Mar 20, 2014, at 1:51 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > >> Hi, >> >> you need to track galaxy-central to make use of the patches that are applied >> as bugfixes after the release. You can do that easily with changing the path >> in .hg/hgrc ... but I do not know if that is the right way to do ;) For me >> it worked. >> >> Cheers, >> Bjoern >> >> Am 20.03.2014 18:46, schrieb Briand, Sheldon: >>> pulling from https://bitbucket.org/galaxy/galaxy-dist >>> searching for changes >>> no changes found >>> >>> From: Greg Von Kuster [mailto:g...@bx.psu.edu] >>> Sent: Thursday, March 20, 2014 2:36 PM >>> To: Briand, Sheldon >>> Cc: 'galaxy-dev@lists.bx.psu.edu' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> There have been several fixes released to the stable branch that you do not >>> have in 12441. I would recommend doing the following: >>> >>> hg pull >>> hg update stable >>> >>> Then uninstall the tophat2 repository and reinstall it. See if that makes >>> a difference. >>> >>> >>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" >>> <sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote: >>> >>> >>> $ hg summary >>> parent: 12441:dc067a95261d >>> >>>> From the tool_dependencies.xml: >>> >>> <package name="tophat2" version="2.0.9"> >>> <repository changeset_revision="8549fd545473" >>> name="package_tophat2_2_0_9" owner="devteam" >>> prior_installation_required="False" toolshed >>> ="http://toolshed.g2.bx.psu.edu"; /> >>> >>> >>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>] >>> Sent: Thursday, March 20, 2014 2:23 PM >>> To: Briand, Sheldon >>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> What version of Galaxy are you running? You want to look in the tophat2 >>> repository directory, not its package dependency. There should be a >>> tool_dependencies.xml file in the tophat2's installation directory >>> hierarchy somewhere. >>> >>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" >>> <sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote: >>> >>> >>> >>> Hi, >>> >>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd54547 >>> 3 >>> contains only: >>> env.sh >>> >>> If that isn't the right place to look let me know. >>> >>> -Sheldon >>> >>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>] >>> Sent: Thursday, March 20, 2014 2:04 PM >>> To: Briand, Sheldon >>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> It looks like your database and file system are out of sync. Your database >>> seems to think you have an installed repository but your file system does >>> not seem to have the repository's installation directory. Can you confirm >>> that this is the case? >>> >>> >>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" >>> <sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote: >>> >>> >>> >>> >>> Hi, >>> >>> Here is the error from the paster.log: >>> >>> Traceback (most recent call last): >>> File >>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", >>> line 496, in handle_tool_dependencies >>> from_install_manager=from_install_manager ) File >>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", >>> line 318, in install_package >>> from_install_manager=from_install_manager ) File >>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", >>> line 245, in handle_complex_repository_d ependency_for_package >>> tool_dependencies_config = >>> get_absolute_path_to_file_in_repository( repo_files_dir, >>> 'tool_dependencies.xml' ) File >>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", >>> line 126, in get_absolute_path_to_file_i n_repository >>> for root, dirs, files in os.walk( repo_files_dir ): >>> File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk >>> names = listdir(top) >>> TypeError: coercing to Unicode: need string or buffer, NoneType >>> found >>> >>> -Sheldon >>> >>> From: >>> galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists. >>> b >>> x.psu.edu> >>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto:dev-bounces@lists. >>> bx.psu.edu>] On Behalf Of Briand, Sheldon >>> Sent: Thursday, March 20, 2014 10:52 AM >>> To: 'Greg Von Kuster' >>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> Hi, >>> >>> Yes the error is: >>> Error installing tool dependency package tophat2 version 2.0.9: >>> coercing to Unicode: need string or buffer, NoneType found >>> >>> -Sheldon >>> >>> From: Greg Von Kuster [mailto:g...@bx.psu.edu] >>> Sent: Thursday, March 20, 2014 10:49 AM >>> To: Briand, Sheldon >>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> You should be able to click on the missing tool dependency and see its >>> installation log. It should show you whatever error is occuring that is >>> not allowing successful installation. >>> >>> Greg Von Kuster >>> >>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" >>> <sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote: >>> >>> Hi, >>> >>> The repair operation doesn't seem to make any difference (I already tried >>> that before emailing). Screenshot of the result attached. >>> >>> -Sheldon >>> >>> >>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>] >>> Sent: Thursday, March 20, 2014 10:26 AM >>> To: Briand, Sheldon >>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>' >>> Subject: Re: [galaxy-dev] tophat2 install >>> >>> Hi Sheldon, >>> >>> I recommend not manually changing any database entries. You should >>> be able to install the repository and all of its dependencies using >>> the Repair Repository feature. See >>> https://wiki.galaxyproject.org/RepairingInstalledRepositories >>> >>> Greg Von Kuster >>> >>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" >>> <sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote: >>> >>> >>> >>> >>> >>> Hi, >>> >>> Just wondering if I can still use the following to fix up my messed up >>> tophat2 install (the install had hung up on me, for 2 hours, and I tried to >>> remove/repair it via the interface). I haven't had problems installing any >>> other tools or packages. I am using postgres but this advice was given 2 >>> years ago to another user and fields may have changed. Thanks for any help! >>> -Sheldon >>> >>> 1. Manually remove the installed repository subdirectory hierarchy from >>> disk. >>> 2. If the repository included any tools, manually remove entries for >>> each of them from the shed_tool-conf.xml file ( or the equivalent file you >>> have configured for handling installed repositories ) 3. Manually update >>> the database using the following command (assuming your installed >>> repository is named 'bcftools_view' and it is the only repository you have >>> installed with that name) - letter capitalization is required: >>> >>> The following assumes you're using postgres: >>> >>> update tool_shed_repository set deleted=True, uninstalled=True, >>> status='Uninstalled', error_message=Null where name = >>> 'bcftools_view'; >>> >>> >>> >>> From: Briand, Sheldon >>> Sent: Wednesday, March 12, 2014 11:44 AM >>> To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> >>> Subject: tophat2 install >>> >>> Hi, >>> >>> I ran into a problem installing tophat2 here: >>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer, >>> NoneType found >>> >>> I have only used the interface to do the installation (no manual deletes). >>> The rest of the dependencies for tophat2 installed just fine. >>> >>> Repairing the repository doesn't make any difference. >>> >>> Thanks! >>> -Sheldon >>> >>> Sheldon Briand >>> NRC Research Computing Support Analyst Research Computing Support / >>> Soutien Informartique a la Recherche Operations, Science Portfolio / >>> Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 >>> Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 >>> 902 426-1677 >>> sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this and other >>> Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>> <Screenshot.png> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this and other >>> Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this and other >>> Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this and other >>> Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this and other >> Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other Galaxy > lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
