Since you have isolated the problem to running on ceph, I'm not sure there is much help we can offer. My understanding is that the posix filesystem part of ceph (as opposed to the object store) is still in development and could have bugs. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Apr 25, 2013 at 7:35 AM, Shun Liang <Shun.Liang@cruk.cam.ac.uk> wrote:

Dear Galaxy Developers,

Here is some more information about the environment I am trying to install Galaxy on. I am using Ubuntu 12.10 on armv7l architecture. I encountered the Import Error problem when I was running Galaxy on the Ceph file system. This is how the Ceph file system is mounted on the machine:

galaxy@arm01-25:~$ mount | grep ceph 10.20.232.4,10.20.232.8,10.20.232.12,10.20.232.16,10.20.232.20:/ on /mnt/ceph type ceph (name=admin,key=client.admin)

I have later tried to install and run Galaxy on the same machine but on a different directory which is within the EXT4 file system mounted on the hard drive. Galaxy runs on that directory without any problem.

I hope this gives some clue to you to solve the problem.

Many thanks,

Shun

________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Shun Liang [Shun.Liang@cruk.cam.ac.uk] Sent: 24 April 2013 14:56 To: galaxy-user@bx.psu.edu Subject: [galaxy-user] ImportError: Unable to run arch-specific checks

Dear Galaxy Developers,

I am trying to run Galaxy on ARM architecture. I am able to scramble the eggs locally. However, I am unable to run Galaxy on my machine as "run.sh" gives an error after some initialization steps:

galaxy@arm01-48:/mnt/ceph/galaxy/galaxy-dist$ ./run.sh Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing data_manager_conf.xml from data_manager_conf.xml.sample Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/shared/ncbi/builds.txt from builds.txt.sample Initializing tool-data/shared/ensembl/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/publicbuilds.txt from publicbuilds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Traceback (most recent call last): File "/mnt/ceph/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory from galaxy.app import UniverseApplication File "/mnt/ceph/galaxy/galaxy-dist/lib/galaxy/app.py", line 17, in <module> from galaxy.visualization.data_providers.registry import DataProviderRegistry File "/mnt/ceph/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module> from galaxy.visualization.data_providers import genome File "/mnt/ceph/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 13, in <module> import numpy File "/mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/__init__.py", line 137, in <module> import add_newdocs File "/mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/core/__init__.py", line 5, in <module> import multiarray ImportError: /mnt/ceph/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-armv7l-ucs4.egg/numpy/core/multiarray.so: Unable to run arch-specific checks

May I ask if anyone has any idea about this error? Many thanks.

Best regards, Shun

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