Hi Greg,

Here is the output of the commands:

hg status

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

hg verify

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

hg summary

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

And hg diff gives a lot of output because of the custom tool configs (290 
unknown files?)

Does this indicate why the changeset_revision can not be determined?


On 06/15/2012 02:58 PM, Greg Von Kuster wrote:
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?



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.


Greg Von Kuster

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


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:

 line 144 in __call__
  app_iter = self.application(environ, sr_checker)
 line 106 in __call__
  environ, self.app)
 line 543 in intercept_output
  app_iter = application(environ, replacement_start_response)
 line 84 in __call__
  return self.application(environ, start_response)
 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 )
 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
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">

Should I put more configuration in this file?

Any help is appreciated.


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