Re: [galaxy-user] Inquiring

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Re: [galaxy-user] Inquiring

Nate Coraor (nate@bx.psu.edu)
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.

Yan Luo wrote:
> Dear Sir,
>
> (1)We installed Galaxy, but recently the user can't registered and got 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
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 = [hidden email]

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 <[hidden email]> 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.
> >
> > Yan Luo wrote:
> > > Dear Sir,
> > >
> > > (1)We installed Galaxy, but recently the user can't registered and got
> > 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
> > > [hidden email]
> > > http://lists.bx.psu.edu/listinfo/galaxy-user
> >
> >


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Re: Inquiring

luoyan
Dear Nate,

It is great suggestion. I copy my root folder of galaxy as follows, could you please let me know if I need to change them to one user "kangtu/admin". I hope we new user register can work today after I restart.

-------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ ls -la
total 1688
drwxr-xr-x 18 junzhu admin 36864 2011-01-28 15:05 .
drwxr-xr-x  4 kangtu admin 36864 2011-01-21 21:44 ..
-rw-r--r--  1 root   root   2882 2011-01-27 02:38 buildbot_setup.sh
-rw-r--r--  1 root   root    352 2011-01-27 02:38 community_datatypes_conf.xml.sample
-rw-r--r--  1 root   root   2170 2011-01-27 02:38 community_wsgi.ini.sample
drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:08 contrib
drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:09 cron
drwxr-xr-x  9 kangtu admin 36864 2011-01-27 02:40 database
-rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml
-rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml.sample
drwxr-xr-x  5 kangtu admin 36864 2011-01-28 06:07 display_applications
-rw-r--r--  1 root   root   7360 2011-01-27 02:38 dist-eggs.ini
drwxr-xr-x 20 kangtu admin 36864 2011-01-28 15:04 eggs
-rw-r--r--  1 root   root   1602 2011-01-27 02:38 eggs.ini
-rwxr-xr-x  1 root   root     65 2011-01-27 02:38 export_history.sh
drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 galaxy_env
drwxr-xr-x  3 kangtu admin 36864 2011-01-28 06:09 .hg
-rw-r--r--  1 root   root    552 2011-01-27 02:38 .hgignore
drwxr-xr-x  4 kangtu admin 36864 2011-02-01 18:22 lib
-rw-r--r--  1 root   root   1254 2011-01-27 02:38 LICENSE.txt
drwxr-xr-x  4 kangtu admin 36864 2011-01-28 06:08 locale
-rw-r--r--  1 root   root    303 2011-01-27 02:38 Makefile
-rwxr-xr-x  1 root   root    238 2011-01-27 02:38 manage_db.sh
-rw-r--r--  1 root   root    507 2011-01-27 02:38 MANIFEST.in
-rw-r--r--  1 root   root    977 2011-01-27 02:38 README.txt
-rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini
-rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini.sample
-rw-r--r--  1 root   root    146 2011-01-27 02:38 run_community.sh
-rwxr-xr-x  1 root   root   1946 2011-01-27 02:38 run_functional_tests.sh
-rw-r--r--  1 root   root    105 2011-01-27 02:38 run_galaxy_listener.sh
-rw-r--r--  1 root   root    140 2011-01-27 02:38 run_reports.sh
-rwxr-xr-x  1 kangtu admin   826 2010-11-01 17:06 run.sh
-rwxr-xr-x  1 root   root    263 2011-01-27 02:38 run_unit_tests.sh
drwxr-xr-x 11 kangtu admin 36864 2011-01-28 06:08 scripts
-rwxr-xr-x  1 root   root     63 2011-01-27 02:38 set_metadata.sh
-rw-r--r--  1 root   root   1499 2011-01-27 02:38 setup.sh
drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 static
drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 templates
drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 test
drwxr-xr-x  8 kangtu admin 90112 2011-01-28 06:13 test-data
-rwxr-xr-x  1 root   root  21748 2011-01-27 02:38 tool_conf.xml
-rw-r--r--  1 root   root  18242 2011-01-27 02:38 tool_conf.xml.main
-rw-r--r--  1 root   root  21300 2011-01-27 02:38 tool_conf.xml.sample
lrwxrwxrwx  1 kangtu admin    28 2010-11-02 09:44 tool-data -> ../galaxy-central/tool-data/
drwxr-xr-x  3 kangtu admin 36864 2011-01-27 02:39 tool-data-bak
-rw-r--r--  1 root   root    878 2011-01-27 02:38 tool_data_table_conf.xml
-rw-r--r--  1 root   root    878 2011-01-27 02:38 tool_data_table_conf.xml.sample
-rw-r--r--  1 root   root   2556 2011-01-27 02:38 tool_list.py
lrwxrwxrwx  1 kangtu admin    23 2010-11-01 17:37 tools -> ../galaxy-central/tools
drwxr-xr-x 37 kangtu admin 36864 2011-01-24 01:49 tools-bak
-rw-r--r--  1 root   root    438 2011-01-27 02:38 transfer_datasets.ini.sample
-rw-r--r--  1 root   root  16421 2011-01-27 02:38 universe_wsgi.ini
-rw-r--r--  1 root   root  16367 2011-01-27 02:38 universe_wsgi.ini.sample
-rw-r--r--  1 root   root  75592 2011-01-27 02:38 virtualenv.py
-rw-r--r--  1 root   root  69811 2011-01-27 02:38 virtualenv.pyc


-----------
I have not checked the subfolder, is it necessary to change all the sub folders and its files. And we also need to reset the all files permission to 777 after I restart galaxy?

Thanks,

Yan


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Re: Inquiring

luoyan
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 <[hidden email]> wrote:
Dear Nate,

It is great suggestion. I copy my root folder of galaxy as follows, could you please let me know if I need to change them to one user "kangtu/admin". I hope we new user register can work today after I restart.

-------------
kangtu@dscbc-compute:~/Downloads/galaxy-dist$ ls -la
total 1688
drwxr-xr-x 18 junzhu admin 36864 2011-01-28 15:05 .
drwxr-xr-x  4 kangtu admin 36864 2011-01-21 21:44 ..
-rw-r--r--  1 root   root   2882 2011-01-27 02:38 buildbot_setup.sh
-rw-r--r--  1 root   root    352 2011-01-27 02:38 community_datatypes_conf.xml.sample
-rw-r--r--  1 root   root   2170 2011-01-27 02:38 community_wsgi.ini.sample
drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:08 contrib
drwxr-xr-x  2 kangtu admin 36864 2011-01-28 06:09 cron
drwxr-xr-x  9 kangtu admin 36864 2011-01-27 02:40 database
-rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml
-rw-r--r--  1 root   root  21698 2011-01-27 02:38 datatypes_conf.xml.sample
drwxr-xr-x  5 kangtu admin 36864 2011-01-28 06:07 display_applications
-rw-r--r--  1 root   root   7360 2011-01-27 02:38 dist-eggs.ini
drwxr-xr-x 20 kangtu admin 36864 2011-01-28 15:04 eggs
-rw-r--r--  1 root   root   1602 2011-01-27 02:38 eggs.ini
-rwxr-xr-x  1 root   root     65 2011-01-27 02:38 export_history.sh
drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 galaxy_env
drwxr-xr-x  3 kangtu admin 36864 2011-01-28 06:09 .hg
-rw-r--r--  1 root   root    552 2011-01-27 02:38 .hgignore
drwxr-xr-x  4 kangtu admin 36864 2011-02-01 18:22 lib
-rw-r--r--  1 root   root   1254 2011-01-27 02:38 LICENSE.txt
drwxr-xr-x  4 kangtu admin 36864 2011-01-28 06:08 locale
-rw-r--r--  1 root   root    303 2011-01-27 02:38 Makefile
-rwxr-xr-x  1 root   root    238 2011-01-27 02:38 manage_db.sh
-rw-r--r--  1 root   root    507 2011-01-27 02:38 MANIFEST.in
-rw-r--r--  1 root   root    977 2011-01-27 02:38 README.txt
-rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini
-rw-r--r--  1 root   root   1994 2011-01-27 02:38 reports_wsgi.ini.sample
-rw-r--r--  1 root   root    146 2011-01-27 02:38 run_community.sh
-rwxr-xr-x  1 root   root   1946 2011-01-27 02:38 run_functional_tests.sh
-rw-r--r--  1 root   root    105 2011-01-27 02:38 run_galaxy_listener.sh
-rw-r--r--  1 root   root    140 2011-01-27 02:38 run_reports.sh
-rwxr-xr-x  1 kangtu admin   826 2010-11-01 17:06 run.sh
-rwxr-xr-x  1 root   root    263 2011-01-27 02:38 run_unit_tests.sh
drwxr-xr-x 11 kangtu admin 36864 2011-01-28 06:08 scripts
-rwxr-xr-x  1 root   root     63 2011-01-27 02:38 set_metadata.sh
-rw-r--r--  1 root   root   1499 2011-01-27 02:38 setup.sh
drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 static
drwxr-xr-x 16 kangtu admin 36864 2011-01-27 02:39 templates
drwxr-xr-x  5 kangtu admin 36864 2011-01-24 01:49 test
drwxr-xr-x  8 kangtu admin 90112 2011-01-28 06:13 test-data
-rwxr-xr-x  1 root   root  21748 2011-01-27 02:38 tool_conf.xml
-rw-r--r--  1 root   root  18242 2011-01-27 02:38 tool_conf.xml.main
-rw-r--r--  1 root   root  21300 2011-01-27 02:38 tool_conf.xml.sample
lrwxrwxrwx  1 kangtu admin    28 2010-11-02 09:44 tool-data -> ../galaxy-central/tool-data/
drwxr-xr-x  3 kangtu admin 36864 2011-01-27 02:39 tool-data-bak
-rw-r--r--  1 root   root    878 2011-01-27 02:38 tool_data_table_conf.xml
-rw-r--r--  1 root   root    878 2011-01-27 02:38 tool_data_table_conf.xml.sample
-rw-r--r--  1 root   root   2556 2011-01-27 02:38 tool_list.py
lrwxrwxrwx  1 kangtu admin    23 2010-11-01 17:37 tools -> ../galaxy-central/tools
drwxr-xr-x 37 kangtu admin 36864 2011-01-24 01:49 tools-bak
-rw-r--r--  1 root   root    438 2011-01-27 02:38 transfer_datasets.ini.sample
-rw-r--r--  1 root   root  16421 2011-01-27 02:38 universe_wsgi.ini
-rw-r--r--  1 root   root  16367 2011-01-27 02:38 universe_wsgi.ini.sample
-rw-r--r--  1 root   root  75592 2011-01-27 02:38 virtualenv.py
-rw-r--r--  1 root   root  69811 2011-01-27 02:38 virtualenv.pyc


-----------
I have not checked the subfolder, is it necessary to change all the sub folders and its files. And we also need to reset the all files permission to 777 after I restart galaxy?

Thanks,

Yan



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Re: Inquiring

luoyan
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

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Re: Inquiring

luoyan
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
 

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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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
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Re: Inquiring

luoyan
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 <[hidden email]> 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


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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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
> >
> >
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Re: Inquiring

luoyan
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 <[hidden email]> 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 <[hidden email]> 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
> >
> >


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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]> 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
> > > >
> > > >
> >
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Re: Inquiring

luoyan
In reply to this post by luoyan
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> >
> >



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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> >> > >
> >> > >
> >>
> >
> >
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Re: Inquiring

luoyan
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

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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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
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Re: Inquiring

luoyan
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 <[hidden email]> 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: <a href="https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]" target="_blank">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


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Re: Inquiring

luoyan
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 <[hidden email]> 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 <[hidden email]> 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



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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]> 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
> >>
> >
> >
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Re: Inquiring

luoyan
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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:
> >> <a href="https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]" target="_blank">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
> >>
> >
> >


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Re: Inquiring

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> > > >>
> > > >
> > > >
> >
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