Hi Team,

I am attempting to rebuild my local instance of galaxy on my Mac since having been upgraded to Mountain Lion.  I have installed Mercurial, postgres, python2.7.  I have cloned the latest galaxy-dist.  However, when I attempted to launch galaxy with sh run.sh it fails to complete the fetch.  Here is what I get:

milkyway:galaxy-dist itw$ sh run.sh
Initializing datatypes_conf.xml from datatypes_conf.xml.sample
Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample
Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing reports_wsgi.ini from reports_wsgi.ini.sample
Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing tool_conf.xml from tool_conf.xml.sample
Initializing shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample
Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample
Initializing data_manager_conf.xml from data_manager_conf.xml.sample
Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing openid_conf.xml from openid_conf.xml.sample
Initializing universe_wsgi.ini from universe_wsgi.ini.sample
Initializing tool-data/shared/ncbi/builds.txt from builds.txt.sample
Initializing tool-data/shared/ensembl/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/publicbuilds.txt from publicbuilds.txt.sample
Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
Initializing tool-data/add_scores.loc from add_scores.loc.sample
Initializing tool-data/alignseq.loc from alignseq.loc.sample
Initializing tool-data/all_fasta.loc from all_fasta.loc.sample
Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample
Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample
Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample
Initializing tool-data/binned_scores.loc from binned_scores.loc.sample
Initializing tool-data/blastdb.loc from blastdb.loc.sample
Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample
Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample
Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample
Initializing tool-data/codingSnps.loc from codingSnps.loc.sample
Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample
Initializing tool-data/faseq.loc from faseq.loc.sample
Initializing tool-data/funDo.loc from funDo.loc.sample
Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample
Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample
Initializing tool-data/liftOver.loc from liftOver.loc.sample
Initializing tool-data/maf_index.loc from maf_index.loc.sample
Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample
Initializing tool-data/microbial_data.loc from microbial_data.loc.sample
Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample
Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample
Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample
Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample
Initializing tool-data/phastOdds.loc from phastOdds.loc.sample
Initializing tool-data/picard_index.loc from picard_index.loc.sample
Initializing tool-data/quality_scores.loc from quality_scores.loc.sample
Initializing tool-data/regions.loc from regions.loc.sample
Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample
Initializing tool-data/sam_fa_new_indices.loc from sam_fa_new_indices.loc.sample
Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample
Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample
Initializing tool-data/sift_db.loc from sift_db.loc.sample
Initializing tool-data/srma_index.loc from srma_index.loc.sample
Initializing tool-data/twobit.loc from twobit.loc.sample
Initializing static/welcome.html from welcome.html.sample
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.4.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/Babel/Babel-0.9.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/amqplib/amqplib-0.6.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-0.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg
Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg
Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/wchartype/wchartype-0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/elementtree/elementtree-1.2.6_20050316-py2.7.egg
Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg
Fetched http://eggs.galaxyproject.org/boto/boto-2.5.2-py2.7.egg
Fetched http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
    egg.resolve()
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py", line 565, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: mercurial==2.2.3
Fetch failed.

I have also tried to run python ./scripts/fetch_eggs.py and get the following:

milkyway:galaxy-dist itw$ python ./scripts/fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.
Dependency "ssh" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
    egg.resolve()
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
    dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
  File "/Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
    raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/itw/work/Galaxy/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4'))


I have looked through the Dev site and have found nothing that helps.  Any ideas are welcome.

Thanks,

Iry Witham

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