Question: (Closed) Galaxy Installation on Freebsd 10.0
gravatar for ashishtx
5.4 years ago by
United States
ashishtx0 wrote:

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

# 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Some eggs are out of date, attempting to fetch...Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a dependent egg of bioblend) cannot be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/ -e simplejsonFetch failed.Traceback (most recent call last): File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/", line 38, in app_factory from import UniverseApplication File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/", line 12, in <module> from galaxy.visualization.data_providers.registry import DataProviderRegistry File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/", line 2, in <module> from galaxy.visualization.data_providers import genome File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/", 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/", 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/ Undefined symbol "__ks_insertsort_heap"

So I have tried running this script
python scripts/ -e simplejson

Traceback (most recent call last): File "scripts/", line 50, in <module> egg.scramble() File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/", 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,, 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".

Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility issues?

Thanks you.

tool galaxy software error • 1.8k views
ADD COMMENTlink modified 5.4 years ago by SES8.3k • written 5.4 years ago by ashishtx0
gravatar for Istvan Albert
5.4 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

Hello ashishtx!

We believe that this post does not fit the main topic of this site.

Please post the question on the Galaxy User support site (also based on Biostar):

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD COMMENTlink written 5.4 years ago by Istvan Albert ♦♦ 82k
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