Toolshed tool doesn't exist error after installation from toolshed

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Toolshed tool doesn't exist error after installation from toolshed

Simon Gladman
Hi all,

Looked for this in the list but couldn't find it. Admittedly I was using gmail to search the list so I may have missed it - apologies if so.

I have put a very simple tool into a local toolshed (latest version of toolshed) which just consists of an xml wrapper and a perl script in the repository. (attached) I want to test it prior to putting it in the main toolshed..

When I install the tool into my galaxy (latest-stable version) it installs ok.

I then go to run the tool and it loads the interface quite happily but upon execute it says tool doesn't exist.

I think its looking in the wrong folder on the server for the tool.

In the main galaxy window: 

Tool 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' does not exist, kwd={'tool_state': u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e', 'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'}

In the server log:

galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434 index called with tool id 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' but no such tool exists
128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] "POST /tool_runner/index HTTP/1.1" 200 - "https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.edu.au%3A9009/repos/slugger/fasta_stats/fasta-stats/1.0.0" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.110 Safari/537.36"

The tool is installed in (via the toolshed install process):


Any ideas?

Cheers,

Simon Gladman


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Re: Toolshed tool doesn't exist error after installation from toolshed

Greg Von Kuster
Hi Simon,

I just installe dour fasta_stats repository form the test tool shed and successfully executed your fast statistics tool, so I am not able to reproduce this behavior.  There must be a configuration problem in your local Galaxy instance that is resulting in this behavior, but I cannot tell you what it is.  The problem seems to be that your fasta statistics tool is not properly loaded into your Galaxy tool box, so your paster log should show an exception when attempting to load the tool after the repository is installed.  Here's what my paster log shows, what does yours show?

Thanks,

Greg Von Kuster

127.0.0.1 - - [11/Jun/2013:08:52:49 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8763/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 Firefox/21.0"
127.0.0.1 - - [11/Jun/2013:08:53:15 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=ea3d74feddb3e781&changeset_revisions=3eca3cb79e74 HTTP/1.1" 200 - "http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ea3d74feddb3e781&changeset_revision=3eca3cb79e74" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 Firefox/21.0"
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,794 Loading new tool panel section: fasta
tool_shed.util.shed_util_common DEBUG 2013-06-11 08:53:20,794 Adding new row (or updating an existing row) for repository 'fasta_stats' in the tool_shed_repository table.
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,835 Appending to tool panel section: fasta
127.0.0.1 - - [11/Jun/2013:08:53:20 -0400] "POST /admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=7f7b0676b166777988637e98c4b4cf254cac31b0%3A7b2266617374615f7374617473223a205b2250726f647563652062617369632073746174697374696373206f6e20612066617374612f6d756c746966617374612066696c65222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f73696d6f6e2d676c61646d616e2f66617374615f7374617473222c2022336563613363623739653734222c202231222c202273696d6f6e2d676c61646d616e222c207b7d2c207b7d5d7d&includes_tools=True&tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=False HTTP/1.1" 200 - "http://localhost:8763/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=ea3d74feddb3e781&changeset_revisions=3eca3cb79e74" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 Firefox/21.0"
/Users/gvk/workspace/galaxy-central/lib/tool_shed/util/xml_util.py:90: FutureWarning: The behavior of this method will change in future versions.  Use specific 'len(elem)' or 'elem is not None' test instead.
  if elem:
galaxy.tools DEBUG 2013-06-11 08:53:21,609 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0, version: 1.0.0 into tool panel.



On Jun 11, 2013, at 12:37 AM, Simon Gladman <[hidden email]> wrote:

Hi all,

Looked for this in the list but couldn't find it. Admittedly I was using gmail to search the list so I may have missed it - apologies if so.

I have put a very simple tool into a local toolshed (latest version of toolshed) which just consists of an xml wrapper and a perl script in the repository. (attached) I want to test it prior to putting it in the main toolshed..

When I install the tool into my galaxy (latest-stable version) it installs ok.

I then go to run the tool and it loads the interface quite happily but upon execute it says tool doesn't exist.

I think its looking in the wrong folder on the server for the tool.

In the main galaxy window: 

Tool 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' does not exist, kwd={'tool_state': u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e', 'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'}

In the server log:

galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434 index called with tool id 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' but no such tool exists
128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] "POST /tool_runner/index HTTP/1.1" 200 - "https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.edu.au%3A9009/repos/slugger/fasta_stats/fasta-stats/1.0.0" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.110 Safari/537.36"

The tool is installed in (via the toolshed install process):


Any ideas?

Cheers,

Simon Gladman

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___________________________________________________________
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:
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