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 <luomails@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