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.sz@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.baker@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.sz@gmail.com> wrote:
Could someone please take a look?
Thanks, Rui
On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI <ruiwang.sz@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
<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#> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*983* in
<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*(*
<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#>
⇝ 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#> 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#> 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#> 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#> parts*.*append*(* arg*.*strip*(* '/' *)* *)* *AttributeError: 'NoneType' object has no attribute 'strip'*
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