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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