Just a hunch, do you guys think pysam is the cause of these issues?
From: ashishtx(a)hotmail.com
To: dannon.baker(a)gmail.com
CC: galaxy-dev(a)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(a)gmail.com
To: ashishtx(a)hotmail.com
CC: galaxy-dev(a)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(a)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 simplejsonTraceback (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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