Dayananda,
The tool data directory should have been created upon running galaxy the first
time. Does galaxy user have write access to this filesystem? The first thing
to check would be to inspect the galaxy directory and see what's actually
there. Does ' /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/tool-data' exist,
and is anything in it?
-Dannon
On Jul 6, 2011, at 7:28 PM, Dayananda Sagar wrote:
> Hello,
> My name is Dayananda Sagar Gangadharaiah and I am a computational
> biology research associate at the University of Nebraska, Lincoln.
> We have been trying to install Galaxy for running a software tool called
> KIRMES. We are encountering the following errors when we run Galaxy using sh
> ./run.sh command
>
> ERROR: Unable to read builds file: [Errno 2] No such file or directory:
> '/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared
> /ucsc/builds.txt'
> ERROR: Unable to read builds for site file
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt
> ERROR: Unable to read builds for site file
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/gbrowse/gbrowse_build_sites.t
> xt
> ERROR: Unable to read builds for site file
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/genetrack/genetrack_sites.txt
> python path is:
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/
> pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
> /mnt/nfs/software/pkgs/
> TFBS/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-li
> nux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkg
> s/TFBS/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/ga
> laxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
> /mnt/nfs/software/pkgs/TFB
> S/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs2.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
> /mnt/nfs/softwar
> e/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg,
> /
> mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.
> egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
> /mnt/
> nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2
> .egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.
> 6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib,
> /arch/lib/python2.6/site-pack
> ages/setuptools-0.6c11-py2.6.egg,
> /arch/lib/python2.6/site-packages/pip-1.0.1-py2.6.egg,
> /arch/lib/python26.zip, /arch/lib/python2.6, /arch/lib/python2.6/plat-li
> nux2, /arch/lib/python2.6/lib-tk, /arch/lib/python2.6/lib-old,
> /arch/lib/python2.6/lib-dynload,
> /mnt/nfs/software/software/64-bit/lib/python2.6/site-packages
> Traceback (most recent call last):
> File
> "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/app.py",
> line 20, in __init__
> self.config.check()
> File "/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/config.py",
> line 174, in check
> raise ConfigurationError("Directory does not exist: %s" % path )
> ConfigurationError: Directory does not exist:
> /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/tool-data
>
>
> Since we do not work on Python we are not able to rectify these problems.
> Please help us in fixing these errors.
>
> Regards,
>
> Dayananda Sagar Gangadharaiah
> E115, Beadle Center
> University of Nebraska- Lincoln
> 1901 Vine St., Lincoln, NE 68588-0665
> Phone: (402) 472-8236
> ___________________________________________________________
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