Hello Galaxy! I can actually confirm this issue in my macbook air after fetching a fresh clone from galaxy-dist (a few minutes ago) and running a:
$ rm -rf eggs/* && ./run.sh (… many correctly fetched eggs… ) 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/roman/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/roman/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/roman/dev/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/roman/.venvburrito/lib/python/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 596, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: mercurial==2.2.3 Fetch failed. Immediately after running the command above, re-running ./run.sh gives: Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: SQLAlchemy (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/roman/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/roman/dev/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/roman/.venvburrito/lib/python/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 600, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/roman/dev/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed. So I tried to upgrade virtualenv-burrito, just in case it was a problem with its pkg_resources being outdated?: $ virtualenv-burrito update Everything is up to date. Then unsetted PYTHONPATH to use MacOSX's python base installation but same error appeared: $ unset PYTHONPATH 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/roman/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/roman/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/roman/dev/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 "/Library/Python/2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 588, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: mercurial==2.2.3 Fetch failed. Apparently the correct eggs are up there in the galaxy egg repo: http://eggs.galaxyproject.org/mercurial/ I checked pull requests and bug reports first in trello, but there doesn't seem to be a ticket for this one. Cheers! Roman 16 jul 2013 kl. 20:59 skrev Iry Witham <iry.wit...@jax.org>: > 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 > The information in this email, including attachments, may be confidential and > is intended solely for the addressee(s). If you believe you received this > email by mistake, please notify the sender by return email as soon as > possible. > ___________________________________________________________ > 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: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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