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
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Dannon Baker -
Dayananda Sagar