Just a hunch, do you guys think  pysam is the cause of these issues?
From: ashis...@hotmail.com
To: dannon.ba...@gmail.com
CC: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Installing Galaxy on Freebsd 10.0
Date: Wed, 10 Sep 2014 19:21:33 -0500




Hi Dannon,
Thanks for the reply. 
====================================================================================##
 python --version








Python 2.7.3# cd galaxy-dist*# rm -rf eggs#python scripts/fetch_eggs.py    
/*Running this command after deleting egg folder */ 








Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg
Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.13-py2.7.egg
Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-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
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
    egg.resolve()
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, 
in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/usr/home/ec2-user/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 "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 565, in 
resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: PyYAML==3.10
==============================================================================================================

I ran the command again without deleting the "egg" folder and this is what I 
got 
==============================================================================================================#python
 scripts/fetch_eggs.py     /*Running this command 2nd time  without deleting 
egg folder */








Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: pytz (a dependent egg of Babel) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-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 "paramiko" 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 "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
    egg.resolve()
  File "/usr/home/ec2-user/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 "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 569, in 
resolve
    raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 
(/usr/home/ec2-user/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), 
Requirement.parse('pycrypto>=2.1,!=2.4'))=================================================================================================================
Can you think of any other reasons? It works well on OS X and Ubuntu. 

-Ashish


Date: Wed, 10 Sep 2014 16:59:13 -0400
Subject: Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0
From: dannon.ba...@gmail.com
To: ashis...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

Hey Ashish,
We have an open issue to sort out exactly why/how this happens, but a quick fix 
for many users is just to remove your eggs/ folder and all eggs and re-run 
`python scripts/fetch_eggs.py`.  Give that a shot, but do let me know if it 
doesn't' work.

On Wed, Sep 10, 2014 at 4:54 PM, ashish damania <ashis...@hotmail.com> wrote:



# sh run.shSome eggs are out of date, attempting to fetch...Warning: setuptools 
(a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a 
dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be 
downloaded automatically. You can trybuilding it by hand with: python 
scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call 
last): File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
38, in app_factory from galaxy.app import UniverseApplication File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in <module> from 
galaxy.visualization.data_providers.registry import DataProviderRegistry File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
 line 2, in <module> from galaxy.visualization.data_providers import genome 
File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
 line 17, in <module> from pysam import !csamtools, ctabix File 
"/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/pysam/__init__.py",
 line 1, in <module> from csamtools import *ImportError: 
/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/csamtools.so:
 Undefined symbol "__ks_insertsort_heap"So I have tried running this 
scriptpython scripts/scramble.py -e simplejson‚ÄčTraceback (most recent call 
last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in 
scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to 
fail, but no egg found to copy from expected path:\n %s" % ( 
sys._getframe().f_code.co_name, self.name, new_egg ) 
)galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson did 
not appear to fail, but no egg found to copy from expected path: 
/usr/home/ec2-user/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.eggI
 found that I have file named: 
"simplejson-2.1.1-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg" in the 
"../scripts/scramble/build/py2.7/simplejson/dist/" folder. I renamed that file 
simplejson-2.1.1-py2.7.egg but it gives me that same error when I execute "sh 
run.sh".Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility 
issues?Thanks you.                                        

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