Re: [galaxy-dev] Galaxy ego fetching error (Mac OS X 10.8)

2013-07-26 Thread Roman Valls Guimera
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Some eggs are out of date, attempting to fetch...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
 

[galaxy-dev] Galaxy ego fetching error (Mac OS X 10.8)

2013-07-16 Thread Iry Witham
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