Just a hunch, do you guys think  pysam is the cause of these issues?


From: ashishtx@hotmail.com
To: dannon.baker@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.baker@gmail.com
To: ashishtx@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 <ashishtx@hotmail.com> wrote:
# sh run.sh
Some 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 script
python scripts/scramble.py -e simplejson

Traceback (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.egg


I 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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