Installing Galaxy on Freebsd 10.0

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Installing Galaxy on Freebsd 10.0

kasperset
# 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Some eggs are out of date, attempting to fetch...Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a dependent egg of bioblend) cannot be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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Re: Installing Galaxy on Freebsd 10.0

Dannon Baker-2
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 <[hidden email]> 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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Re: Installing Galaxy on Freebsd 10.0

kasperset
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: [hidden email]
To: [hidden email]
CC: [hidden email]

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 <[hidden email]> 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.

___________________________________________________________
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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Installing Galaxy on Freebsd 10.0

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


From: [hidden email]
To: [hidden email]
CC: [hidden email]
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: [hidden email]
To: [hidden email]
CC: [hidden email]

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 <[hidden email]> 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.

___________________________________________________________
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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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