M run.sh
M static/fastx_icons/barcode_splitter_output_example.png
M static/fastx_icons/fasta_clipping_histogram_1.png
M static/fastx_icons/fasta_clipping_histogram_2.png
M static/fastx_icons/fastq_nucleotides_distribution_1.png
M static/fastx_icons/fastq_nucleotides_distribution_2.png
M static/fastx_icons/fastq_nucleotides_distribution_3.png
M static/fastx_icons/fastq_nucleotides_distribution_4.png
M static/fastx_icons/fastq_quality_boxplot_1.png
M static/fastx_icons/fastq_quality_boxplot_2.png
M static/fastx_icons/fastq_quality_boxplot_3.png
M static/fastx_icons/fastx_clipper_example.png
M test-data/fasta_collapser1.out
M test-data/fastq_stats1.fastq
M test-data/fastx_barcode_splitter1.out
M test-data/fastx_clipper1a.out
M tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh
M tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
M tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
M tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
M tools/sr_mapping/bowtie_wrapper.xml
M tools/sr_mapping/bwa_wrapper.xml
? core
? datatypes_conf.xml.bak
? jobs/pp_rjcnfq0
? lib/galaxy/datatypes/metagenomics.py
? lib/galaxy/datatypes/registry.py.bak
? paster.log
? paster.pid
? scripts/set_metadata.py.bak
? static/fastx_icons/fastq_nucleotides_distribution_line_graph.png
? static/images/cloud.gif
? static/images/cloud_text.png
...

checking changesets
checking manifests
crosschecking files in changesets and manifests
checking files
5932 files, 7277 changesets, 28530 total revisions

parent: 7276:622fd4f0a437 tip
 Fix bug in packing track that is a library dataset
branch: default
commit: 22 modified, 290 unknown
update: (current)

Hi Matthias,

There is really nothing to configure in your Galaxy environment in order to use the public Galaxy tool sheds.  Ideally, you should set the following configuration setting, but not setting it defaults to using the file named shed_tool_conf.xml for installed tools anyway.

tool_config_files = tool_conf.xml,shed_tool_conf.xml

The current Galaxy central repository tip is 7276:622fd4f0a437, which you should pull.  This is the revision that the public tool sheds are using - they generally always run the Galaxy central tip revision.

It's very possible that since you updated after 6 months of development, your repository has some issues.  What are the results of the following commands?

hg diff

hg status

hg verify

hg summary

On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote:

Hi Greg,

I guess something went wrong while update, because I updated to the
latest changeset:

hg tip | grep changeset
changeset:   7262:4fbd05095ca7

Can it be because I the last time I updated was at least half a year ago
and the toolshed integration has been implemented afterwards? So that I
need to configure the toolshed before I can install something form the
public one?

Thanks!

Mattias


On 06/13/2012 05:43 PM, Greg Von Kuster wrote:

Hello Mattias,

Did you pull from the Galaxy central repo?  The latest change set is 7262:4fbd05095ca7, which is what you should be running in order to use the tool shed.  Let me know if you in fact have the latest from central - your line numbers in your log below look to be different from mine.

Thanks,

Greg Von Kuster

On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote:

Hi,

I just updated my local Galaxy installation to the latest version. I am

trying out the feature to add tools directly from the toolshed, but this

is not working. It results in this error:

File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__

  app_iter = self.application(environ, sr_checker)

File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__

  environ, self.app)

File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output

  app_iter = application(environ, replacement_start_response)

File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__

  return self.application(environ, start_response)

File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__

  return self.application(environ, start_response)

File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__

  body = method( trans, **kwargs )

File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator

  return func( self, trans, *args, **kwargs )

File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 481 in install_repository

  install_tool_dependencies=install_tool_dependencies )

File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 1228 in load_repository_contents

  dist_to_shed=False )

File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 342 in create_or_update_tool_shed_repository

  installed_changeset_revision=changeset_revision,

NameError: global name 'changeset_revision' is not defined

And my shed_tools_conf.xml looks like this:

<?xml version="1.0"?>

<toolbox tool_path="../shed_tools">

</toolbox>

Should I put more configuration in this file?

Any help is appreciated.

Thanks!

Mattias

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