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-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Shun Liang
[shun.li...@cruk.cam.ac.uk]
Sent: 24 April 2013 14:56
To: galaxy-u...@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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