Hi Yan, I've again moved this back to the galaxy-dev list. Please reply to this list and not galaxy-user. Yan Luo wrote:
Dear Nate,
Thanks for your quick response. I appreciate, it is very important for us to use it. We have problem recently.
(1) In fact, I can't find the file "paster.log". The problem is that recently we expanded our gluster(Linux sever) and did the rebalance that has some bugs. Some of files permission have been changed. So we can't use User/register righr now, when we tried, we got the sever error, do you have any idea how to fix it? (we can change the ownships/read and write permission for some files manually, but we don't know which files and where they are?)
If you are executing run.sh without the --daemon flag, the output will go to whatever terminal window you started Galaxy in, not to a file. You'll want to make sure that all of the files under Galaxy's root directory are owned by a single user, which is the same user which starts and runs the Galaxy process.
(2) We want to reboot the Galaxy, should we first stop and start as follows? $ sh run.sh --stop $ sh run.sh
The full command to stop would be `sh run.sh --stop-daemon`, but that only applies if you originally started Galaxy with `run.sh --daemon`.
Is there any difference if I use "-daemon" flag? Last times, my colleague started using "./run.sh". How to stop it? If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find the process (Linux) that is running by Galaxy and kill it?
The --daemon flag runs Galaxy in the background and redirects its output to paster.log. Without the --daemon flag, the process stays connected to the terminal in which you start it. Since Galaxy wasn't originally started with the --daemon flag, you'll need to find the process, either by locating the terminal window in which it was started (possibly by your colleague) and then hitting Ctrl-C, or by using the `ps` command (e.g. `ps auxwww | grep python`) and killing the Galaxy process. It usually looks something like: nate 18213 0.9 0.4 438844 146260 pts/7 Sl+ 10:47 2:30 python ./scripts/paster.py serve universe_wsgi.ini So you would do: % kill 18213
(3) Could you please let me know if there is a default administrator user/password for galaxy. I want to add an administrator user, how can I do that? According to the instruction, I will change a line of "universe_wsgi.ini" as follows. How can I set/get my password? admin_users = yan.luo@email.com
There is no default. Any users set in admin_uesrs will be administrators. If the account specified in admin_users does not yet exist, you can simply create it. Once created, that account will be an administrator.
(4) I found our "universe_wsgi.ini" contains the following setting, should I remove "#" before this line, stop and start galaxy? #allow_user_creation = True
No, True is the default setting so with it commented it is still set to True.
I plan to restart our galaxy, if it is possible, could you please let me know your phone #? I can call you sometime today, or if you prefer, I can give you my phone #.
Unfortunately, we don't have the resources for phone support. We'll be happy to help via email as much as possible. --nate
Looking forward to hearing from you.
Best Wishes,
Yan Luo, Ph.D. NIH
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Yan,
I've moved this discussion to the galaxy-dev list since it pertains to a local installation of Galaxy.
Responses to your questions follow, in-line.
Dear Sir,
(1)We installed Galaxy, but recently the user can't registered and got
Yan Luo wrote: the
following error, how can we fix it?
Sever error An error occurred. See the error logs for more information.(To turn debug on to display ...).
Since debug = False in universe_wsgi.ini, you should be able to find a more detailed error message in the log file. If starting Galaxy with:
% sh run.sh --daemon
The default log file is 'paster.log' in Galaxy's root directory.
(2) Could you please let me know if there is any command to stop galaxy?
If starting with the --daemon flag (as above), you can use:
% sh run.sh --stop-daemon
If running in the foreground, you can use Ctrl-C to terminate the process. There is a recent bug whereby Ctrl-C is ineffective on some platforms under Python 2.6 - in this case you will have to kill/pkill the process manually. We are working on a fix for the latter.
(3) If I reset universe_wsgi.ini file and want to set an administrator user(I can add a line in the above file), how can I get the password? Should I stop galaxy(See question 2) first? then run "./setup.sh" and "./run.sh".
setup.sh would have only been necessary prior to running Galaxy the first time, however, this step has recently been removed. If you are referencing documentation that still refers to setup.sh, please let us know so we can update it - I did notice this was still on the "Production Server" page, so I removed it from there.
You no longer need to run setup.sh at all.
(4) If I run "setup.sh", will a new file "universe_wsgi.ini" be generated? if I want to change this file,should I edit it before "run.sh" and after "setup.sh". Is it right?
setup.sh and its replacements in run.sh and the Galaxy application itself never overwrite files, they only create files from sample files if they do not exist.
(5) I read some of your docs, command "sh setup.sh"(sh run.sh) and "./setup.sh"(./run.sh), which one is correct under Linux?
Both syntaxes are effectively the same in most cases.
--nate
Looking forward to hearing from you.
Best Wises,
Yan Luo, Ph.D. NIH <
http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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
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
Dear Nate, I got the new errors as follows: (I tried ./run.sh) perationalError: (OperationalError) FATAL: Ident authentication failed for user "root" Could you please let me know asap? I am waiting for your answer. Looking forward to hearing from you. Thanks, Yan
Dear Nate, Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible. ---------------- Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/controllers/tracks.py", line 23, in <module> from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/visualization/tracks/data/array_tree.py", line 8, 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 ---------------- Looking forward to hearing from you. Best Wishes, Yan
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible.
Hi Yan, Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here. To ensure there are no permissions problems, please do the following, all as the same non-root user: 1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh` And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on: http://usegalaxy.org/production --nate
---------------- Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/web/controllers/tracks.py", line 23, in <module> from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/lib/galaxy/visualization/tracks/data/array_tree.py", line 8, 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 ----------------
Looking forward to hearing from you.
Best Wishes,
Yan
Dear Nate, Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist" lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/ from "/home/kangtu/data", we have other link as follows. lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu They worked well before, when we just restarted, it has such problem, I couldn't start. By the way, 1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db). 2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320). Looking forward to hearing from you. Thanks, Yan On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist"
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu
They worked well before, when we just restarted, it has such problem, I couldn't start. By the way,
1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db).
Okay, this should be fine.
2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320).
You would need to recompile whatever depends on numpy, which in this case is bx-python. However, we provide our own version of numpy 1.3. The reason that version is not being used is due to a bug in our dependency management code which was just fixed. There are two ways to solve this problem. The first would be to set up a virtualenv as suggested in my last email. The second would be to pull our in-development code, but be aware that this has undergone very little testing at this point. You can pull the most recent changes with: % hg pull -u http://bitbucket.org/galaxy/galaxy-central/ --nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Dear Nate, Thanks for your quick response, my colleagues of a small group are waiting for using galaxy, so it is better if we can restart it asap. 1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I am not familiar with "Python", if we need to do it, could you please let me know how to do it step by step? 2. I checked your instruction you mentioned, will I follow the following steps (a, b, and c)? If it is, I will try immediately. ------------------------------------------- (a) download: nate@weyerbacher% wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py --11:18:05-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py => `virtualenv.py' Resolving bitbucket.org... 184.73.244.143, 184.73.226.175 Connecting to bitbucket.org|184.73.244.143|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 68,601 (67K) [text/x-python] 100%[====================================>] 68,601 --.--K/s 11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601] (b) run command as follows nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env New python executable in galaxy_env/bin/python2.6 Also creating executable in galaxy_env/bin/python Installing setuptools...............done. (c)run the following 3 commands nate@weyerbacher% . ./galaxy_env/bin/activate nate@weyerbacher% cd galaxy_dist nate@weyerbacher% sh run.sh ------------------------------------------ Looking forward to hearing from you. Best Wishes, Yan On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist"
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu
They worked well before, when we just restarted, it has such problem, I couldn't start. By the way,
1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db).
Okay, this should be fine.
2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320).
You would need to recompile whatever depends on numpy, which in this case is bx-python. However, we provide our own version of numpy 1.3. The reason that version is not being used is due to a bug in our dependency management code which was just fixed.
There are two ways to solve this problem. The first would be to set up a virtualenv as suggested in my last email.
The second would be to pull our in-development code, but be aware that this has undergone very little testing at this point. You can pull the most recent changes with:
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart
is
stopped. I hope we can get the solution from you as soon as possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, my colleagues of a small group are waiting for using galaxy, so it is better if we can restart it asap.
1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I am not familiar with "Python", if we need to do it, could you please let me know how to do it step by step?
You will not need to recompile bx-python.
2. I checked your instruction you mentioned, will I follow the following steps (a, b, and c)? If it is, I will try immediately. ------------------------------------------- (a) download:
nate@weyerbacher% wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py --11:18:05-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py => `virtualenv.py' Resolving bitbucket.org... 184.73.244.143, 184.73.226.175 Connecting to bitbucket.org|184.73.244.143|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 68,601 (67K) [text/x-python]
100%[====================================>] 68,601 --.--K/s
11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601]
You should be able to run this exactly as stated.
(b) run command as follows nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env New python executable in galaxy_env/bin/python2.6 Also creating executable in galaxy_env/bin/python Installing setuptools...............done.
Your path to python might be different. Since you have a suitable python interpreter on your $PATH already you can just use: % python virtualenv.py --no-site-packages galaxy_env Note that the `galaxy_env` directory will be created in whatever directory you are currently in, so you probably want to make sure this location makes sense. Perhaps run the command from `/home/kangtu/data/tools`.
(c)run the following 3 commands nate@weyerbacher% . ./galaxy_env/bin/activate nate@weyerbacher% cd galaxy_dist nate@weyerbacher% sh run.sh
This should be fine. --nate
------------------------------------------
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist"
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu
They worked well before, when we just restarted, it has such problem, I couldn't start. By the way,
1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db).
Okay, this should be fine.
2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320).
You would need to recompile whatever depends on numpy, which in this case is bx-python. However, we provide our own version of numpy 1.3. The reason that version is not being used is due to a bug in our dependency management code which was just fixed.
There are two ways to solve this problem. The first would be to set up a virtualenv as suggested in my last email.
The second would be to pull our in-development code, but be aware that this has undergone very little testing at this point. You can pull the most recent changes with:
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart
is
stopped. I hope we can get the solution from you as soon as possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Dear Nate, Sorry for a lot of questions. To set up virtualenv, should I enter the root folder of "galaxy-dist" and run the commands for steps "a", "b" and "c"? For step "b", I only need to run "python virtualenv.py --no-site-packages galaxy_env " from root folder of "galaxy-dist"(don't need to run "/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env"), is it right? You mentioned I need to run command from "/home/kangtu/data/tools" /home/kangtu/Downloads/Galaxy-dist --> /home/kangtu/data/tools/galaxy-dist/ By the way, I found a folder called "galaxy_env" from root folder of "galaxy-dist" form the both folder, they are same (date, time, and size ), can I run step "b" directly from "/home/kangtu/Downloads/Galaxy-dist"? drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 galaxy_env For step "c", is there a space in the beginning? I plan to run it from folder of "galaxy-dist" ". ./galaxy_env/bin/activate" or "../galaxy_env/bin/activate" Looking forward to hearing from you. Best Wishes, Yan On Fri, Feb 11, 2011 at 9:00 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
Thanks for your quick response, my colleagues of a small group are waiting for using galaxy, so it is better if we can restart it asap.
1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I am not familiar with "Python", if we need to do it, could you please let me know how to do it step by step?
2. I checked your instruction you mentioned, will I follow the following steps (a, b, and c)? If it is, I will try immediately. ------------------------------------------- (a) download:
nate@weyerbacher% wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
--11:18:05-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py => `virtualenv.py' Resolving bitbucket.org... 184.73.244.143, 184.73.226.175
Connecting to bitbucket.org|184.73.244.143|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 68,601 (67K) [text/x-python]
100%[====================================>] 68,601 --.--K/s
11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601]
(b) run command as follows nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env New python executable in galaxy_env/bin/python2.6
Also creating executable in galaxy_env/bin/python Installing setuptools...............done.
(c)run the following 3 commands nate@weyerbacher% . ./galaxy_env/bin/activate nate@weyerbacher% cd galaxy_dist
nate@weyerbacher% sh run.sh
------------------------------------------
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist"
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu
They worked well before, when we just restarted, it has such problem, I couldn't start. By the way,
1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db).
Okay, this should be fine.
2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320).
You would need to recompile whatever depends on numpy, which in this case is bx-python. However, we provide our own version of numpy 1.3. The reason that version is not being used is due to a bug in our dependency management code which was just fixed.
There are two ways to solve this problem. The first would be to set up a virtualenv as suggested in my last email.
The second would be to pull our in-development code, but be aware that this has undergone very little testing at this point. You can pull the most recent changes with:
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart
stopped. I hope we can get the solution from you as soon as
is possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems
as
though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Yan Luo wrote:
Dear Nate,
Sorry for a lot of questions. To set up virtualenv, should I enter the root folder of "galaxy-dist" and run the commands for steps "a", "b" and "c"?
For step "b", I only need to run "python virtualenv.py --no-site-packages galaxy_env " from root folder of "galaxy-dist"(don't need to run "/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env"), is it right?
Yes. You can just run: % python virtualenv.py --no-site-packages galaxy_env
You mentioned I need to run command from "/home/kangtu/data/tools"
/home/kangtu/Downloads/Galaxy-dist --> /home/kangtu/data/tools/galaxy-dist/
Using `/home/kangtu/data/tools` was only a suggestion. You may create galaxy_env in whatever directory is most convenient for you.
By the way, I found a folder called "galaxy_env" from root folder of "galaxy-dist" form the both folder, they are same (date, time, and size ), can I run step "b" directly from "/home/kangtu/Downloads/Galaxy-dist"? drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 galaxy_env
It would appear that someone already set up a virtualenv, unless this directory is something else. I don't know the specifics of your system or who did what.
For step "c", is there a space in the beginning? I plan to run it from folder of "galaxy-dist"
". ./galaxy_env/bin/activate" or "../galaxy_env/bin/activate"
The space is intentional. The single '.' is analagous to 'source' in Bash but is compatible with other non-bash shells like Bourne and Dash (Debian). See the "SHELL BUILTIN COMMANDS" section of the bash(1) man page for an explanation. You could simply try these commands out as I suggested and then report back if there are any problems. --nate
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 9:00 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
Thanks for your quick response, my colleagues of a small group are waiting for using galaxy, so it is better if we can restart it asap.
1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I am not familiar with "Python", if we need to do it, could you please let me know how to do it step by step?
2. I checked your instruction you mentioned, will I follow the following steps (a, b, and c)? If it is, I will try immediately. ------------------------------------------- (a) download:
nate@weyerbacher% wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
--11:18:05-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py => `virtualenv.py' Resolving bitbucket.org... 184.73.244.143, 184.73.226.175
Connecting to bitbucket.org|184.73.244.143|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 68,601 (67K) [text/x-python]
100%[====================================>] 68,601 --.--K/s
11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601]
(b) run command as follows nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env New python executable in galaxy_env/bin/python2.6
Also creating executable in galaxy_env/bin/python Installing setuptools...............done.
(c)run the following 3 commands nate@weyerbacher% . ./galaxy_env/bin/activate nate@weyerbacher% cd galaxy_dist
nate@weyerbacher% sh run.sh
------------------------------------------
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from "/home/kangtu/Downloads/galaxy-dist"
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> /home/kangtu/data/tools/galaxy-dist/
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> /mnt/gluster-vol/home/kangtu
They worked well before, when we just restarted, it has such problem, I couldn't start. By the way,
1. I have found some files as "root:root" under "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I changed all them as "kangtu/admin", there is only one user right now (we use postgresql db).
Okay, this should be fine.
2. My colleague told me that he upgraded "numpy" to new version recently, is it the problem? how can we fix it? I checked online, someone said we need to recompile something (http://projects.scipy.org/numpy/ticket/1320).
You would need to recompile whatever depends on numpy, which in this case is bx-python. However, we provide our own version of numpy 1.3. The reason that version is not being used is due to a bug in our dependency management code which was just fixed.
There are two ways to solve this problem. The first would be to set up a virtualenv as suggested in my last email.
The second would be to pull our in-development code, but be aware that this has undergone very little testing at this point. You can pull the most recent changes with:
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart
stopped. I hope we can get the solution from you as soon as
is possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems
as
though there are quite a few copies of Galaxy in use here.
To ensure there are no permissions problems, please do the following, all as the same non-root user:
1. Remove the ~/.python-eggs directory and all of its contents. 2. Clone a new copy of Galaxy. 3. Start Galaxy using `./run.sh`
And report back any errors which persist. If the numpy error below remains, I suggest setting up a Python virtualenv as described on:
http://usegalaxy.org/production
--nate
Dear Nate, I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).) ------------------- kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following] --2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1' [ <=> ] 75,592 --.-K/s in 0.04s 2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] ------------------------------------------- When I checked the root folder of "galaxy-dist", and found: -rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py". Best Wishes, Yan
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write. virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following] --2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at: /home/kangtu/data/tools/galaxy_env or: /home/kangtu/data/tools/galaxy-dist/galaxy_env Whichever it is, do the following: % . /home/kangtu/data/tools/galaxy_env/bin/activate or: % . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate Then: % cd ~/Downloads/galaxy-dist % ./run.sh --nate
Best Wishes,
Yan
Dear Nate, I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run activate and get message: kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo Should I first install it? when I check the above folder, I do find the file 'activate' kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ Could you please let me know if you have any suggestion? Best WIshes, Yan On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following] --2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
Best Wishes,
Yan
Dear Nate, When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly, kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must install "activate", run it, and then "./run.sh" Best Wishes, Yan On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run activate and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following] --2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must install "activate", run it, and then "./run.sh"
The syntax you used above: % . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate Is correct. Executing `activate` directly as in your previous email is incorrect. activate is not an executable, it is a shell environment file which is meant to be sourced with the `.` command. Since you have properly sourced `activate` as shown above, you can now execute `./run.sh`. --nate
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run activate and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following] --2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
Best Wishes,
Yan
Dear Nate, It is running, I am a little nervous, hope it is well. By the way, I forgot set it to the background. If it can start, should I kill the process again, start screen, and './run.sh'? Do I need any activate and "./run/sh"? Thanks for your help, I hope it is smooth. Best Wishes, Yan On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must install "activate", run it, and then "./run.sh"
The syntax you used above:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Is correct. Executing `activate` directly as in your previous email is incorrect. activate is not an executable, it is a shell environment file which is meant to be sourced with the `.` command.
Since you have properly sourced `activate` as shown above, you can now execute `./run.sh`.
--nate
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run
activate
and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location:
https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]
--2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
It is running, I am a little nervous, hope it is well. By the way, I forgot set it to the background. If it can start, should I kill the process again, start screen, and './run.sh'? Do I need any activate and "./run/sh"?
If you close the terminal in which Galaxy is running, Galaxy will stop. You can prevent this using screen as you have suggested, or the --daemon/--stop-daemon method I mentioned in an earlier email. You will need to source `activate` before you run Galaxy if you start a new shell (for example, starting screen). You can see whether it's necessary by looking at the prompt. If your prompt looks like this: kangtu@dscbc-compute:~$ Your virtualenv is not activated. As you can see from the output, once activated your shell prompt will look like: (galaxy_env)kangtu@dscbc-compute:~$ --nate
Thanks for your help, I hope it is smooth.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must install "activate", run it, and then "./run.sh"
The syntax you used above:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Is correct. Executing `activate` directly as in your previous email is incorrect. activate is not an executable, it is a shell environment file which is meant to be sourced with the `.` command.
Since you have properly sourced `activate` as shown above, you can now execute `./run.sh`.
--nate
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run
activate
and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to "wget" and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have permission to write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
-------------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py [sudo] password for kangtu: --2011-02-11 09:36:31-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 Connecting to bitbucket.org|207.223.240.182|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location:
https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]
--2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|207.223.240.182|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in 0.04s
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] -------------------------------------------
When I checked the root folder of "galaxy-dist", and found:
-rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc
Should I chang something for step b "python virtualenv.py --no-site-packages galaxy_env"? for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your previous emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
Best Wishes,
Yan
Dear Nate, It is great, it started. Thanks you very much for your help, otherwise I will spend very long time to handle it. I will ctrl-c the process, activate, and './run.sh'. I hope it will still work and let you know. Best Wishes, Yan On Fri, Feb 11, 2011 at 10:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
It is running, I am a little nervous, hope it is well. By the way, I forgot set it to the background. If it can start, should I kill the process again, start screen, and './run.sh'? Do I need any activate and "./run/sh"?
If you close the terminal in which Galaxy is running, Galaxy will stop. You can prevent this using screen as you have suggested, or the --daemon/--stop-daemon method I mentioned in an earlier email.
You will need to source `activate` before you run Galaxy if you start a new shell (for example, starting screen). You can see whether it's necessary by looking at the prompt. If your prompt looks like this:
kangtu@dscbc-compute:~$
Your virtualenv is not activated. As you can see from the output, once activated your shell prompt will look like:
(galaxy_env)kangtu@dscbc-compute:~$
--nate
Thanks for your help, I hope it is smooth.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute
Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must
install
"activate", run it, and then "./run.sh"
The syntax you used above:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Is correct. Executing `activate` directly as in your previous email is incorrect. activate is not an executable, it is a shell environment file which is meant to be sourced with the `.` command.
Since you have properly sourced `activate` as shown above, you can now execute `./run.sh`.
--nate
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com>
wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run
activate
and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote: > Dear Nate, > > I just run the first step and must use sudo to "wget" and it is ok. > Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have
to
write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
> ------------------- > > kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget > http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > [sudo] password for kangtu: > --2011-02-11 09:36:31-- > http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 > Connecting to bitbucket.org|207.223.240.182|:80... connected. > HTTP request sent, awaiting response... 301 Moved Permanently > Location:
https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]
> --2011-02-11 09:36:31-- > https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > Connecting to bitbucket.org|207.223.240.182|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: unspecified [text/x-python] > Saving to: `virtualenv.py.1' > > [ <=> ] 75,592 --.-K/s in 0.04s > > 2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] > ------------------------------------------- > > When I checked the root folder of "galaxy-dist", and found: > > -rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py > -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 > -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc > > Should I chang something for step b "python virtualenv.py --no-site-packages > galaxy_env"? > for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or > rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your
:~/Downloads/galaxy-dist/galaxy_env/bin$ permission previous
emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
> > Best Wishes, > > Yan
Dear Nate, I just used "screen", and restarted the galaxy, it works. It is perfect, and I also found that some features can't be used before, when I restart it, everything is fine. Have a wonderful weekend! Best Wishes, Yan
Dear Nate, I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem? kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini Looking forward to hearing from you. Best Wishes, yan On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is perfect, and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is. --nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is perfect, and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Dear Nate, Thanks for your quick response, I got "sever error". and just killed the process. When I ran activate as follows and can't active it: kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$ Any suggestion will be appreciate. Best Wishes, Yan On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is
perfect,
and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed the process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad, possibly due to an error with the NFS server. I suggest contacting a local system administrator for assistance. --nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is
perfect,
and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Dear Nate, Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works. Thanks, Yan On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed the process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad, possibly due to an error with the NFS server. I suggest contacting a local system administrator for assistance.
--nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it
well.
This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43
worked python
./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com>
wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is
perfect,
and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works.
Assuming nothing else has changed, it sounds like your NFS server is having some performance problems. --nate
Thanks,
Yan
On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed the process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad, possibly due to an error with the NFS server. I suggest contacting a local system administrator for assistance.
--nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it
well.
This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43
worked python
./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com>
wrote:
Dear Nate,
I just used "screen", and restarted the galaxy, it works. It is
perfect,
and I also found that some features can't be used before, when I restart it, everything is fine.
Have a wonderful weekend!
Best Wishes,
Yan
Dear Nate, We have a new issue to use Galaxy. When we login use a general user account, we found: (1) When we upload six fastq files via URL, three of them can be uploaded successfully while the other three can't be uploaded. (2) What's more, even those files can be uploaded, we can't perform the mapping with BWA (NGS: Mapping/Map with BWA) either single end or paired-end. The problem is we can't select which file to do the mapping. (3) If we use an admin account, we can find one file when we perform the mapping and are trying uploading other one to see if we can select from the two files list. (4) Could you please let me know if Galaxy has some restriction for files number, a single file size, or total files size loaded by one user(account)? Please find the attached screenshoots for your reference. Looking forward to hearing from you. Best Wishes, Yan On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works.
Assuming nothing else has changed, it sounds like your NFS server is having some performance problems.
--nate
Thanks,
Yan
On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed
process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad,
the possibly
due to an error with the NFS server. I suggest contacting a local system administrator for assistance.
--nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Yan Luo wrote:
Dear Nate,
I have a new problem, last week, I restarted the Galaxy, but it
well.
This morning, I found I can't start it from browser, but when I check "ps auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43
worked python
./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
Looking forward to hearing from you.
Best Wishes,
yan
On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com>
wrote:
> Dear Nate, > > I just used "screen", and restarted the galaxy, it works. It is
perfect,
> and I also found that some features can't be used before, when I restart it, > everything is fine. > > Have a wonderful weekend! > > Best Wishes, > > Yan > > >
Dear Nate and developers, Could you please let me know if you have any solution for my questions and several attachments sent to you last week? Someone web pages don't work well. Looking forward to hearing from you. Best Wishes, Yan On Mon, Feb 28, 2011 at 4:45 PM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
We have a new issue to use Galaxy. When we login use a general user account, we found:
(1) When we upload six fastq files via URL, three of them can be uploaded successfully while the other three can't be uploaded.
(2) What's more, even those files can be uploaded, we can't perform the mapping with BWA (NGS: Mapping/Map with BWA) either single end or paired-end. The problem is we can't select which file to do the mapping.
(3) If we use an admin account, we can find one file when we perform the mapping and are trying uploading other one to see if we can select from the two files list.
(4) Could you please let me know if Galaxy has some restriction for files number, a single file size, or total files size loaded by one user(account)?
Please find the attached screenshoots for your reference.
Looking forward to hearing from you.
Best Wishes,
Yan
On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works.
Assuming nothing else has changed, it sounds like your NFS server is having some performance problems.
--nate
Thanks,
Yan
On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed
process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad,
due to an error with the NFS server. I suggest contacting a local system administrator for assistance.
--nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Yan Luo wrote: > Dear Nate, > > I have a new problem, last week, I restarted the Galaxy, but it
worked
well. > This morning, I found I can't start it from browser, but when I check "ps > auxwww|grep python", I still find it is running, what is
the possibly problem?
What happens when you try to connect via a browser? Is an error
displayed? Connection timeout?
> > kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43
message python
> ./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
> > > Looking forward to hearing from you. > > Best Wishes, > > yan > > On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote: > > > Dear Nate, > > > > I just used "screen", and restarted the galaxy, it works. It is perfect, > > and I also found that some features can't be used before, when I restart it, > > everything is fine. > > > > Have a wonderful weekend! > > > > Best Wishes, > > > > Yan > > > > > >
Yan Luo wrote:
Dear Nate,
We have a new issue to use Galaxy. When we login use a general user account, we found:
(1) When we upload six fastq files via URL, three of them can be uploaded successfully while the other three can't be uploaded.
Hi Yan, Could you expand the history items so it's possible to see what the upload error is? If you set the 'smtp_server' and 'error_email_to' options in the universe_wsgi.ini file, you will also get a new icon in the history item which will allow you to generate a bug report. This bug report will contain the full error message from the upload tool, if the one in the history item is truncated.
(2) What's more, even those files can be uploaded, we can't perform the mapping with BWA (NGS: Mapping/Map with BWA) either single end or paired-end. The problem is we can't select which file to do the mapping.
The reason the files are not showing up in the tool most likely has to do with file format. The BWA tool expects input files to be in the fastqsanger format. The best way to acheive this is to run your input file through the FASTQ Groomer tool before using it with BWA.
(3) If we use an admin account, we can find one file when we perform the mapping and are trying uploading other one to see if we can select from the two files list.
(4) Could you please let me know if Galaxy has some restriction for files number, a single file size, or total files size loaded by one user(account)?
Galaxy does not have any built-in limitations on file size/count. --nate
Please find the attached screenshoots for your reference.
Looking forward to hearing from you.
Best Wishes,
Yan
On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works.
Assuming nothing else has changed, it sounds like your NFS server is having some performance problems.
--nate
Thanks,
Yan
On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your quick response, I got "sever error". and just killed
process. When I ran activate as follows and can't active it:
kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$
It looks like the NFS mount on which Galaxy lives has gone bad,
the possibly
due to an error with the NFS server. I suggest contacting a local system administrator for assistance.
--nate
Any suggestion will be appreciate.
Best Wishes,
Yan
On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Yan Luo wrote: > Dear Nate, > > I have a new problem, last week, I restarted the Galaxy, but it
well. > This morning, I found I can't start it from browser, but when I check "ps > auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a browser? Is an error message displayed? Connection timeout?
> > kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43
worked python
> ./scripts/paster.py serve universe_wsgi.ini
If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is.
--nate
> > > Looking forward to hearing from you. > > Best Wishes, > > yan > > On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo <luomails@gmail.com> wrote: > > > Dear Nate, > > > > I just used "screen", and restarted the galaxy, it works. It is perfect, > > and I also found that some features can't be used before, when I restart it, > > everything is fine. > > > > Have a wonderful weekend! > > > > Best Wishes, > > > > Yan > > > > > >
Dear Nate, I can't start my galaxy and got the following information, could you please let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today. File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.6/SocketServer.py", line 400, in __init__ self.server_bind() File "/usr/lib/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use Looking forward to hearing from you. Best Wishes, Yan
Yan Luo wrote:
Dear Nate,
I can't start my galaxy and got the following information, could you please let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today.
File "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed. Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process. --nate
Looking forward to hearing from you.
Best Wishes,
Yan
Dear Nate, Your suggestion is very important for us. You are right, there is other instance of Galaxy to use the socket. I found the ps and kill them, but they are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release the previous port and reuse it in the future version? Have a nice weekend! Best Wishes, Yan On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
I can't start my galaxy and got the following information, could you
Yan Luo wrote: please
let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today.
File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
Your suggestion is very important for us. You are right, there is other instance of Galaxy to use the socket. I found the ps and kill them, but they are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release the previous port and reuse it in the future version?
It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C. Note that screen is not necessary. You can start and stop Galaxy in the background with: Start: % sh run.sh --daemon Stop: % sh run.sh --stop-daemon --nate
Have a nice weekend!
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
I can't start my galaxy and got the following information, could you
Yan Luo wrote: please
let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today.
File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
Dear Nate, Thanks for your information, I will use it next times. By the way, how do we know the status of Galaxy's database (mysql)? I can't make sure if the database starts normally. Best Wishes, Yan On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
Your suggestion is very important for us. You are right, there is other instance of Galaxy to use the socket. I found the ps and kill them, but
are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release
Yan Luo wrote: they the
previous port and reuse it in the future version?
It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C.
Note that screen is not necessary. You can start and stop Galaxy in the background with:
Start:
% sh run.sh --daemon
Stop:
% sh run.sh --stop-daemon
--nate
Have a nice weekend!
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
I can't start my galaxy and got the following information, could you
Yan Luo wrote: please
let me know how we can fix it as soon as possible? We were running
system, it was down last night suddenly. Hope we can fix it today.
File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what
the that
process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
Yan Luo wrote:
Dear Nate,
Thanks for your information, I will use it next times. By the way, how do we know the status of Galaxy's database (mysql)? I can't make sure if the database starts normally.
Do you mean the database server itself? If you can connect with the 'mysql' command line interface, it's up. If you are worried about corruption, you can check the MySQL logs or use 'mysqlcheck'. --nate
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
Your suggestion is very important for us. You are right, there is other instance of Galaxy to use the socket. I found the ps and kill them, but
are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release
Yan Luo wrote: they the
previous port and reuse it in the future version?
It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C.
Note that screen is not necessary. You can start and stop Galaxy in the background with:
Start:
% sh run.sh --daemon
Stop:
% sh run.sh --stop-daemon
--nate
Have a nice weekend!
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Dear Nate,
I can't start my galaxy and got the following information, could you
Yan Luo wrote: please
let me know how we can fix it as soon as possible? We were running
system, it was down last night suddenly. Hope we can fix it today.
File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already listening on the port you are trying to start Galaxy on. You can determine what
the that
process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
Dear Nate, Thanks a lot, I will check them. Best Wishes, Yan On Fri, Apr 1, 2011 at 11:07 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your information, I will use it next times. By the way, how do we know the status of Galaxy's database (mysql)? I can't make sure if the database starts normally.
Do you mean the database server itself? If you can connect with the 'mysql' command line interface, it's up. If you are worried about corruption, you can check the MySQL logs or use 'mysqlcheck'.
--nate
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Your suggestion is very important for us. You are right, there is
instance of Galaxy to use the socket. I found the ps and kill them, but they are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release the previous port and reuse it in the future version?
It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C.
Note that screen is not necessary. You can start and stop Galaxy in
background with:
Start:
% sh run.sh --daemon
Stop:
% sh run.sh --stop-daemon
--nate
Have a nice weekend!
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Yan Luo wrote:
Dear Nate,
I can't start my galaxy and got the following information, could
please
let me know how we can fix it as soon as possible? We were running
you the
system, it was down last night suddenly. Hope we can fix it today.
File
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper **context.local_conf) ... File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already
other the listening on
the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
Hi, Nate, How are you? Last week our director attended a meeting at New York and got some information from you. I just visited your homepage " http://galaxy.psu.edu/" he mentioned. We have some question to "Use Galaxy<http://usegalaxy.org/>" and "Get Galaxy <http://getgalaxy.org/>". We want to figure out how our PIs at NIH can use them. Do you have any information regarding the 2 above issues? for example, slides, introduction, and links, etc. 1. Which servers are available for users to use right now? Are they free? Is there any restriction? for example, file size, speed, etc. 2. Is there any difference between "local version" and "cloud version"? What are they different and benefits? Please let me know if you have any suggestion. Best Wishes, Yan On Fri, Apr 1, 2011 at 11:12 AM, Yan Luo <luomails@gmail.com> wrote:
Dear Nate,
Thanks a lot, I will check them.
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 11:07 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Thanks for your information, I will use it next times. By the way, how do we know the status of Galaxy's database (mysql)? I can't make sure if the database starts normally.
Do you mean the database server itself? If you can connect with the 'mysql' command line interface, it's up. If you are worried about corruption, you can check the MySQL logs or use 'mysqlcheck'.
--nate
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
Your suggestion is very important for us. You are right, there is
instance of Galaxy to use the socket. I found the ps and kill them, but they are still there, then I using screen -wipe to remove it (I use screen to run the galaxy). It works. Is there any possibly for Galaxy to auto release the previous port and reuse it in the future version?
It does this now. You would need to reconnect to the screen (using 'screen -r') and stop Galaxy with CTRL-C.
Note that screen is not necessary. You can start and stop Galaxy in
background with:
Start:
% sh run.sh --daemon
Stop:
% sh run.sh --stop-daemon
--nate
Have a nice weekend!
Best Wishes,
Yan
On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Yan Luo wrote: > Dear Nate, > > I can't start my galaxy and got the following information,
please > let me know how we can fix it as soon as possible? We were running
could you the
> system, it was down last night suddenly. Hope we can fix it today. > > > > File >
"/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 151, in server_wrapper > **context.local_conf) ... > File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind > self.socket.bind(self.server_address) > File "<string>", line 1, in bind > socket.error: [Errno 98] Address already in use
Something (possibly another instance of Galaxy) is already
other the listening on
the port you are trying to start Galaxy on. You can determine what that process is with 'lsof -i :<PORT>' where <PORT> is the port number you connect to Galaxy on. You may need to use sudo for this to succeed.
Assuming it's another Galaxy instance, you can probably find it with 'ps auxwww | grep universe' and then kill that process.
--nate
> > > > > > Looking forward to hearing from you. > > Best Wishes, > > Yan
Yan, 1. Right now, we host and you can use usegalaxy.org ( main.g2.bx.psu.edu ), and test.bx.psu.edu. Main will be the most reliable server and what we recommend you use, but test has a few beta tools that aren't available on main yet. That said, test.g2.bx.psu.edu is very much for testing and breaking and shouldn't be used without acknowledging that. 2. A local galaxy instance is hosted locally, on your server(s). If you have a local compute cluster or even a single beefy server that you can access and use, this is free, but comes with the caveat that you actually run and administer your own servers, install required tools, etc. A cloud galaxy instance is hosted on Amazon EC2, and comes with most tools and many common indices installed and preconfigured. The downside to this is that it does cost money ( http://aws.amazon.com/ec2/pricing/ ) to run EC2 instances based on your needs. There's a lot more I can point out if you're interested in running your own galaxy in the cloud, but I would tentatively suggest that you experiment with our main galaxy server at usegalaxy.org, and potentially migrate to a local and/or cloud solution as your analysis needs demand. Thanks! Dannon On Nov 7, 2011, at 6:33 PM, Yan Luo wrote:
Hi, Nate,
How are you? Last week our director attended a meeting at New York and got some information from you. I just visited your homepage "http://galaxy.psu.edu/" he mentioned. We have some question to "Use Galaxy" and "Get Galaxy". We want to figure out how our PIs at NIH can use them. Do you have any information regarding the 2 above issues? for example, slides, introduction, and links, etc.
1. Which servers are available for users to use right now? Are they free? Is there any restriction? for example, file size, speed, etc.
2. Is there any difference between "local version" and "cloud version"? What are they different and benefits?
Please let me know if you have any suggestion.
Best Wishes,
Yan
participants (3)
-
Dannon Baker -
Nate Coraor -
Yan Luo