Galaxy Installation on Freebsd 10.0

Question: Galaxy Installation on Freebsd 10.0

4.2 years ago by

United States

ashishtx • 10 wrote:

I am trying to install Galaxy under Freebsd version 10.0 but I keep getting this error ( See below)

# 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Some eggs are out of date, attempting to fetch...Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a dependent egg of bioblend) cannot be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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modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by ashishtx • 10

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