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