[galaxy-user] Problems installing Galaxy

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[galaxy-user] Problems installing Galaxy

Rodolfo Aramayo
People,

Apologies for the disturbance.

On a fresh MacOSX I installed Python, Numpy and Scipy using MacPorts

I tested both Numpy and Scipy as follows:

==
   python
   >>> import numpy
   >>> numpy.test('1','10')
   >>> import scipy
   >>> scipy.test('1','10')
==

The computer does understand them and processes them as expected. The
tests seem to work?

However, when I attempt a fresh installation of Galaxy I get the
following error:

> hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
requesting all changes
adding changesets
adding manifests
adding file changes
added 3787 changesets with 17203 changes to 4176 files
updating to branch default
2691 files updated, 0 files merged, 0 files removed, 0 files unresolved

>sh setup.sh
Copying datatypes_conf.xml.sample to datatypes_conf.xml
Copying reports_wsgi.ini.sample to reports_wsgi.ini
Copying tool_conf.xml.sample to tool_conf.xml
Copying universe_wsgi.ini.sample to universe_wsgi.ini
Copying tool-data/alignseq.loc.sample to tool-data/alignseq.loc
Copying tool-data/annotation_profiler_options.xml.sample to
tool-data/annotation_profiler_options.xml
Copying tool-data/annotation_profiler_valid_builds.txt.sample to
tool-data/annotation_profiler_valid_builds.txt
Copying tool-data/binned_scores.loc.sample to tool-data/binned_scores.loc
Copying tool-data/blastdb.loc.sample to tool-data/blastdb.loc
Copying tool-data/bowtie_indices.loc.sample to tool-data/bowtie_indices.loc
Copying tool-data/encode_datasets.loc.sample to tool-data/encode_datasets.loc
Copying tool-data/liftOver.loc.sample to tool-data/liftOver.loc
Copying tool-data/maf_index.loc.sample to tool-data/maf_index.loc
Copying tool-data/maf_pairwise.loc.sample to tool-data/maf_pairwise.loc
Copying tool-data/microbial_data.loc.sample to tool-data/microbial_data.loc
Copying tool-data/phastOdds.loc.sample to tool-data/phastOdds.loc
Copying tool-data/quality_scores.loc.sample to tool-data/quality_scores.loc
Copying tool-data/regions.loc.sample to tool-data/regions.loc
Copying tool-data/sam_fa_indices.loc.sample to tool-data/sam_fa_indices.loc
Copying tool-data/sequence_index_base.loc.sample to
tool-data/sequence_index_base.loc
Copying tool-data/sequence_index_color.loc.sample to
tool-data/sequence_index_color.loc
Copying tool-data/twobit.loc.sample to tool-data/twobit.loc
Copying tool-data/shared/ucsc/builds.txt.sample to
tool-data/shared/ucsc/builds.txt
Creating database/files
Creating database/community_files
Creating database/tmp
Creating database/compiled_templates
Creating database/job_working_directory
Creating database/pbs
Creating static/genetrack/plots
Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/new/docutils/docutils-0.4-py2.6.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 31, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py",
line 284, in resolve
    egg.resolve()
  File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py",
line 172, in resolve
    r = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py",
line 551, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: numpy==1.3.0
>
Any Ideas?

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