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*(* 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#>
⇝ 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#> parts*.*append*(* arg*.*strip*(* '/' *)* *)* *AttributeError: 'NoneType' object has no attribute 'strip'*
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