Dear Nate,

I just tried to start, but get some error, I used "./run.sh"

kangtu@dscbc-compute:~/Downloads/galaxy-central$ sudo ./run.sh
Traceback (most recent call last):
  File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-central/lib/galaxy/web/buildapp.py",
line 81, in app_factory
    from galaxy.app import UniverseApplication
  File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-central/lib/galaxy/app.py", line
11, in <module>
    from galaxy.tools.imp_exp import load_history_imp_exp_tools
  File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-central/lib/galaxy/tools/imp_exp/__init__.py",
line 6, in <module>
    from galaxy.web.base.controller import UsesHistory
  File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-central/lib/galaxy/web/base/controller.py",
line 12, in <module>
    from galaxy.visualization.tracks.data_providers import get_data_provider
  File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-central/lib/galaxy/visualization/tracks/data_providers.py",
line 9, in <module>
    from bx.arrays.array_tree import FileArrayTreeDict
  File "numpy.pxd", line 119, in init bx.arrays.array_tree
(lib/bx/arrays/array_tree.c:11323)
ValueError: numpy.dtype does not appear to be the correct type object
kangtu@dscbc-compute:~/Downloads/galaxy-central$
---


Could you please give me any suggestion?

Thanks,

Yan

On Thu, Feb 10, 2011 at 3:35 PM, Yan Luo <luoma...@gmail.com> wrote:

> Dear Nate,
>
> It is great suggestion. I copy my root folder of galaxy as follows, could
> you please let me know if I need to change them to one user "kangtu/admin".
> I hope we new user register can work today after I restart.
>
> -------------
> kangtu@dscbc-compute:~/Downloads/galaxy-dist$ ls -la
> total 1688
> drwxr-xr-x 18 junzhu admin 36864 2011-01-28 15:05 .
> drwxr-xr-x  4 kangtu admin 36864 2011-01-21 21:44 ..
> -rw-r--r--  1 root   root   2882 2011-01-27 02:38 buildbot_setup.sh
> -rw-r--r--  1 root   root    352 2011-01-27 02:38
> community_datatypes_conf.xml.sample
> -rw-r--r--  1 root   root   2170 2011-01-27 02:38 community_wsgi.ini.sample
> drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:08 contrib
> drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:09 cron
> drwxr-xr-x  9 kangtu admin 36864 2011-01-27 02:40 database
> -rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml
> -rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml.sample
> drwxr-xr-x  5 kangtu admin 36864 2011-01-28 06:07 display_applications
> -rw-r--r--  1 root   root   7360 2011-01-27 02:38 dist-eggs.ini
> drwxr-xr-x 20 kangtu admin 36864 2011-01-28 15:04 eggs
> -rw-r--r--  1 root   root   1602 2011-01-27 02:38 eggs.ini
> -rwxr-xr-x  1 root   root     65 2011-01-27 02:38 export_history.sh
> drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 galaxy_env
> drwxr-xr-x  3 kangtu admin 36864 2011-01-28 06:09 .hg
> -rw-r--r--  1 root   root    552 2011-01-27 02:38 .hgignore
> drwxr-xr-x  4 kangtu admin 36864 2011-02-01 18:22 lib
> -rw-r--r--  1 root   root   1254 2011-01-27 02:38 LICENSE.txt
> drwxr-xr-x  4 kangtu admin 36864 2011-01-28 06:08 locale
> -rw-r--r--  1 root   root    303 2011-01-27 02:38 Makefile
> -rwxr-xr-x  1 root   root    238 2011-01-27 02:38 manage_db.sh
> -rw-r--r--  1 root   root    507 2011-01-27 02:38 MANIFEST.in
> -rw-r--r--  1 root   root    977 2011-01-27 02:38 README.txt
> -rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini
> -rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini.sample
> -rw-r--r--  1 root   root    146 2011-01-27 02:38 run_community.sh
> -rwxr-xr-x  1 root   root   1946 2011-01-27 02:38 run_functional_tests.sh
> -rw-r--r--  1 root   root    105 2011-01-27 02:38 run_galaxy_listener.sh
> -rw-r--r--  1 root   root    140 2011-01-27 02:38 run_reports.sh
> -rwxr-xr-x  1 kangtu admin   826 2010-11-01 17:06 run.sh
> -rwxr-xr-x  1 root   root    263 2011-01-27 02:38 run_unit_tests.sh
> drwxr-xr-x 11 kangtu admin 36864 2011-01-28 06:08 scripts
> -rwxr-xr-x  1 root   root     63 2011-01-27 02:38 set_metadata.sh
> -rw-r--r--  1 root   root   1499 2011-01-27 02:38 setup.sh
> drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 static
> drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 templates
> drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 test
> drwxr-xr-x  8 kangtu admin 90112 2011-01-28 06:13 test-data
> -rwxr-xr-x  1 root   root  21748 2011-01-27 02:38 tool_conf.xml
> -rw-r--r--  1 root   root  18242 2011-01-27 02:38 tool_conf.xml.main
> -rw-r--r--  1 root   root  21300 2011-01-27 02:38 tool_conf.xml.sample
> lrwxrwxrwx  1 kangtu admin    28 2010-11-02 09:44 tool-data ->
> ../galaxy-central/tool-data/
> drwxr-xr-x  3 kangtu admin 36864 2011-01-27 02:39 tool-data-bak
> -rw-r--r--  1 root   root    878 2011-01-27 02:38 tool_data_table_conf.xml
> -rw-r--r--  1 root   root    878 2011-01-27 02:38
> tool_data_table_conf.xml.sample
> -rw-r--r--  1 root   root   2556 2011-01-27 02:38 tool_list.py
> lrwxrwxrwx  1 kangtu admin    23 2010-11-01 17:37 tools ->
> ../galaxy-central/tools
> drwxr-xr-x 37 kangtu admin 36864 2011-01-24 01:49 tools-bak
> -rw-r--r--  1 root   root    438 2011-01-27 02:38
> transfer_datasets.ini.sample
> -rw-r--r--  1 root   root  16421 2011-01-27 02:38 universe_wsgi.ini
> -rw-r--r--  1 root   root  16367 2011-01-27 02:38 universe_wsgi.ini.sample
> -rw-r--r--  1 root   root  75592 2011-01-27 02:38 virtualenv.py
> -rw-r--r--  1 root   root  69811 2011-01-27 02:38 virtualenv.pyc
>
>
> -----------
> I have not checked the subfolder, is it necessary to change all the sub
> folders and its files. And we also need to reset the all files permission to
> 777 after I restart galaxy?
>
> Thanks,
>
> Yan
>
>
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