That's correct -- none of them are run automatically.
On Wed, Aug 6, 2014 at 3:08 PM, Beginner TI <ruiwang...@gmail.com> wrote: > Ah, I think that I had a wrong impression before...so by default, the > migration scripts listed here will NOT be executed, am I correct? I think > that 'done' at the bottom made me think that it was executed... > > So it's the user's responsibility to execute those scripts, correct? > > Thanks, > Rui > > The Emboss 5.0.0 tools have been eliminated from the distribution and the > Emboss datatypes have been removed fromdatatypes_conf.xml.sample. You should > remove the Emboss datatypes from your version of datatypes_conf.xml. > Therepositories named emboss_5 and emboss_datatypes from the main Galaxy Tool > Shed at http://toolshed.g2.bx.psu.eduwill be installed into your local Galaxy > instance at the location discussed above by running the following > command.vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvsh > ./scripts/migrate_tools/0002_tools.sh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^doneAfter > the installation process finishes, you can start your Galaxy server. As part > of this installation process,entries for each of the following tool config > files will be added to the file named ./migrated_tool_conf.xml, so thesetools > will continue to be loaded into your tool panel. Because of this, existing > entries for these files should beremoved from your file named > ./tool_conf.xml, but only after the installation process finishes. > > > > On Wed, Aug 6, 2014 at 10:53 AM, Dannon Baker <dannon.ba...@gmail.com> > wrote: > >> Ahh, I think I see the issue. So, many galaxy tools are being migrated >> out of the distribution and to the toolshed -- you can find much more >> detailed information here: >> https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution >> >> The samtools wrappers were migrated in migration 8, I think, if that >> helps. >> >> Basically, there's a migration script that should have shown up in a >> terminal somewhere when you ran your galaxy instance after the update that >> will contain a reference to script(s) that you can run that'll take care of >> the migration. >> >> Let me know if you need more information, if the wiki page doesn't clear >> it up! >> >> -Dannon >> >> >> On Wed, Aug 6, 2014 at 1:36 PM, Beginner TI <ruiwang...@gmail.com> wrote: >> >>> Hi Dannon, >>> >>> Thanks for the reply. Sorry for the duplicate. I was wondering that the >>> original subject sounded like a user problem so I updated it... >>> >>> Actually we are having a little down time right now for a file system >>> check. I'll try your suggestions asap and let you know. At the mean time, >>> could you please elaborate this a little bit? I noticed that in the >>> tool_conf.xml, not every tool is shown on the panel although they are all >>> defined there in the same format. I also noticed that all the tool xml >>> files, such as >>> >>> <section id="samtools" name="NGS: SAM Tools"> >>> <tool file="samtools/sam_bitwise_flag_filter.xml" /> >>> <tool file="samtools/sam2interval.xml" /> >>> <tool file="samtools/sam_to_bam.xml" /> >>> <tool file="samtools/bam_to_sam.xml" /> >>> <tool file="samtools/sam_merge.xml" /> >>> <tool file="samtools/samtools_mpileup.xml" /> >>> <tool file="samtools/sam_pileup.xml" /> >>> <tool file="samtools/pileup_parser.xml" /> >>> <tool file="samtools/pileup_interval.xml" /> >>> <tool file="samtools/samtools_flagstat.xml" /> >>> <tool file="samtools/samtools_rmdup.xml" /> >>> <tool file="samtools/samtools_slice_bam.xml" /> >>> </section> >>> >>> the directory samtools and all these xml files are no longer in the >>> tools directory. seems that upgrade deleted them. is this correct? or they >>> are moved to somewhere else? I looked around but didn't see. >>> >>> Based on this, I think that even I removed the tool_panel.xml file you >>> mentioned, I will still not be able to restore samtools even I could see >>> it...could you please let me know how I could configure this? >>> >>> Thanks, >>> Rui >>> >>> >>> On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker <dannon.ba...@gmail.com> >>> wrote: >>> >>>> Hi Rui, >>>> >>>> We'll definitely take a look. Please allow for a reasonable time >>>> period to pass before sending duplicate emails to the list asking for >>>> assistance. >>>> >>>> That said, does deleting your integrated_tool_panel.xml (this file is >>>> automatically regenerated by Galaxy, safe to remove it and restart) bring >>>> back your manually installed samtools? >>>> >>>> >>>> On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI <ruiwang...@gmail.com> >>>> wrote: >>>> >>>>> Could someone please take a look? >>>>> >>>>> Thanks, >>>>> Rui >>>>> >>>>> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI <ruiwang...@gmail.com> >>>>> wrote: >>>>> >>>>>> Dear Admin, >>>>>> >>>>>> Since the upgrade, I lost the samtools that I installed myself. >>>>>> Although it is still in the tool_conf.xml, it does not show up on the >>>>>> panel. I tried to install from toolshed, but failed. Error messages >>>>>> pasted >>>>>> below. Could someone take a look? >>>>>> >>>>>> Thanks, >>>>>> Rui >>>>>> >>>>>> ⇝ AttributeError: 'NoneType' object has no attribute 'strip' >>>>>> URL: >>>>>> http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977 >>>>>> Module weberror.evalexception.middleware:*364* in respond >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> app_iter *=* self*.*application*(*environ*,* detect_start_response*)* >>>>>> Module paste.recursive:*84* in __call__ >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> *return* self*.*application*(*environ*,* start_response*)* >>>>>> Module paste.httpexceptions:*633* in __call__ >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> *return* self*.*application*(*environ*,* start_response*)* >>>>>> Module galaxy.web.framework.base:*132* in __call__ >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> *return* self*.*handle_request*(* environ*,* start_response *)* >>>>>> Module galaxy.web.framework.base:*190* in handle_request >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> body *=* method*(* trans*,* ****kwargs *)* >>>>>> Module galaxy.web.framework:*369* in decorator >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* >>>>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:*983* in >>>>>> prepare_for_install >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> includes_tool_dependencies *)* >>>>>> Module tool_shed.util.common_install_util:*97* in >>>>>> get_dependencies_for_repository >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> repository *=* suc*.*get_repository_for_dependency_relationship*(* >>>>>> trans*.*app*,* tool_shed_url*,* name*,*repository_owner*,* >>>>>> changeset_revision *)* >>>>>> Module tool_shed.util.shed_util_common:*1036* in >>>>>> get_repository_for_dependency_relationship >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> *(* name*,* owner*,* changeset_revision *)* *)* >>>>>> Module tool_shed.util.shed_util_common:*1867* in url_join >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> view >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> >> >>>>>> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977#> >>>>>> parts*.*append*(* arg*.*strip*(* '/' *)* *)* >>>>>> *AttributeError: 'NoneType' object has no attribute 'strip'* >>>>>> >>>>>> >>>>> >>>>> 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