Mira doesn’t work on Galaxy. This is the log message I receive. Tool: Assemble with MIRA v3.4 Name: MIRA log Created: Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version: 0.0.10 Tool Version: None Tool Standard Output: stdouthttp://130.56.251.91/datasets/d5f55b83db1f410a/stdout Tool Standard Error: stderrhttp://130.56.251.91/datasets/d5f55b83db1f410a/stderr Tool Exit Code: None API ID: d5f55b83db1f410a Full Path: /mnt/galaxy/files/000/dataset_326.dat
Input Parameter Value Note for rerun Assembly method De novo Assembly type Genome Assembly quality grade Accurate Backbones/reference chromosomes? false Sanger/Capillary reads? false 454 reads? false Solexa/Illumina reads? false Ion Torrent reads? true Ion Torrent reads file 10: R_2011_10_19_14_30_56_user_SN1-36_Auto_SN1-36_38.fastq Inheritance Chain MIRA log
Also I can’t install Mira 4. This is the message I receive. Any suggestions.
Thanks.
Marija Tauschek
-- Dr Marija Tauschek/Atanaskovic Robins-Browne Lab Dept Microbiology & Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia Tel: +61 3 8344 9927 Email: matan@unimelb.edu.au Internal Server Error Galaxy was unable to successfully complete your request
URL: http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https:... Module galaxy.web.framework.middleware.error:149 in __call__
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# body = method( trans, **kwargs )
Module galaxy.web.framework:369 in decorator
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:983 in prepare_for_install
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# includes_tool_dependencies )
Module tool_shed.util.common_install_util:97 in get_dependencies_for_repository
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# 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://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# ( name, owner, changeset_revision ) )
Module tool_shed.util.shed_util_common:1867 in url_join
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236# parts.append( arg.strip( '/' ) )
AttributeError: 'NoneType' object has no attribute 'strip' extra datahttp://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236#extra_data
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic matan@unimelb.edu.au wrote:
Mira doesn’t work on Galaxy. This is the log message I receive.
Tool: Assemble with MIRA v3.4 Name: MIRA log Created: Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version: 0.0.10 Tool Version: None Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: None API ID: d5f55b83db1f410a Full Path: /mnt/galaxy/files/000/dataset_326.dat ...
What was the stdout and stderr information?
Did you install this from the main tool shed?: https://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Also I can’t install Mira 4. This is the message I receive. Any suggestions.
Getting "Internal Server Error" is unhelpful - I can't really guess what might be going wrong here :(
I have had problems with the MIRA dependencies when Bastien has renamed folders on sourceforge... are you using the Test Tool Shed here (since I have not yet released the MIRA 4 wrapper on the main ToolShed)?: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Regards,
Peter
On Fri, Aug 22, 2014 at 8:00 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic matan@unimelb.edu.au wrote:
Also I can’t install Mira 4. This is the message I receive. Any suggestions.
Getting "Internal Server Error" is unhelpful - I can't really guess what might be going wrong here :(
This is a guess, but it could be you need to set the https_proxy in the /etc/environment file - see this thread: http://dev.list.galaxyproject.org/Internal-Server-Error-when-trying-to-insta...
Peter
galaxy-dev@lists.galaxyproject.org