On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:I installed galaxy as recommended in the docs:
> Dan,
> Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the
> tip or a specific revision?
>
hg clone https://bitbucket.org/galaxy/galaxy-dist/
OK, now bizarrely I am having a slightly different problem, but AFAIK
> When you see the Syntax error, does Galaxy continue to start up after and
> the upload error (AttributeError: 'NoneType' object has no attribute 'add')
> happens later?
nothing has changed.
I don't get that stack trace on startup and now I can upload pasted
text, but I can't seem to upload files. I tried to upload a 3KB csv
file called sample.csv and it shows up in history with the animated up
arrow but the upload never finishes, and every 4 seconds the log
shows:
127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] "GET
/api/histories/8237ee2988567c1c HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS
X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56No error message in the log though.
Safari/537.17"
So I can at least get past my initial place where I was stuck, because
the tools I am developing need only text files as input (which can be
pasted).
I'd still like to know why I can't upload files (from the Choose File
button on the Upload File page).
Thanks for your help,
Dan
> To make sure I'm understanding you correctly, you can find this error in the
> logs of both of your installations?
>
> Thanks,
> C
>
>
> On Tue, Jan 29, 2013 at 1:55 PM, Carl Eberhard <carlfeberhard@gmail.com>
> wrote:
>>
>> galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner:
>> galaxy.jobs.runners.local:LocalJobRunner
>> galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not
>> loadable: galaxy.jobs.runners.lwr
>> Traceback (most recent call last):
>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
>> line 447, in _load_plugin
>> module = __import__( module_name )
>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
>> line 232
>> worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ),
>> target=self.run_next )
>> ^
>> SyntaxError: invalid syntax
>>
>>
>> It is significant - and not normal behavior. Good catch!
>>
>> (You can disregard the 'Error: this request returned None from
>> get_history()' message; it records the lack of a current history which is
>> normal when you access those pages but haven't logged in yet)
>>
>>
>>
>> On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
>> wrote:
>>>
>>> Hi Carl,
>>>
>>>
>>>
>>> On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard <carlfeberhard@gmail.com>
>>> wrote:
>>> > Those are both fine then.
>>> >
>>> > You've got us (temporarily) stumped - even the old timers here.
>>> >
>>> > Can you give some rough information on your system - what OS you're
>>> > using,
>>> > what your network set up would be?
>>> >
>>>
>>> Thanks again for looking into this. It's Mac OS X 10.8.2 with Chrome
>>> 24.0.1312.56, though I have the same problems with Safari 6.0.2
>>> (8536.26.17) and Firefox 17.0.
>>> Python 2.7.2.
>>>
>>> > Also - if it's not too problematic - can you do a fresh clone of Galaxy
>>> > onto
>>> > your system and see if that installation has the same problem?
>>> >
>>>
>>> I did this and it seems to have pretty much the same problem but a
>>> slightly different manifestation. Now I am now getting the error
>>> message "Error: this request returned None from get_history():
>>> http://localhost:8080/" when I try and upload a file; instead, no
>>> error messages show up in the console, but the upload still fails. I
>>> do however get that error message when I try and log in as a user
>>> after registering that user.
>>>
>>> Another thing I notice, in the output immediately after starting run.sh:
>>>
>>> galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner:
>>> galaxy.jobs.runners.local:LocalJobRunner
>>> galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not
>>> loadable: galaxy.jobs.runners.lwr
>>> Traceback (most recent call last):
>>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
>>> line 447, in _load_plugin
>>> module = __import__( module_name )
>>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
>>> line 232
>>> worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ),
>>> target=self.run_next )
>>> ^
>>> SyntaxError: invalid syntax
>>>
>>> Maybe that is significant?
>>>
>>> Switching back to my previous distribution I get the identical
>>> behavior...
>>>
>>> Thanks,
>>> Dan
>>>
>>>
>>> > C
>>> >
>>> >
>>> >
>>> >
>>> > On Mon, Jan 28, 2013 at 5:03 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
>>> > wrote:
>>> >>
>>> >> On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard
>>> >> <carlfeberhard@gmail.com>
>>> >> wrote:
>>> >> > If you go to your galaxy root in a terminal and then cd to eggs,
>>> >> > what is
>>> >> > the
>>> >> > version listed for SQLAlchemy?
>>> >> >
>>> >>
>>> >> SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
>>> >>
>>> >>
>>> >> > Do you have SQLAlchemy installed already on that machine (apart from
>>> >> > the
>>> >> > one
>>> >> > in Galaxy's eggs)?
>>> >> >
>>> >>
>>> >> I don't think so. I never knowingly installed it and in a fresh python
>>> >> session, 'import sqlalchemy' returns an error that there is no such
>>> >> module.
>>> >>
>>> >> Thanks,
>>> >> Dan
>>> >>
>>> >>
>>> >> >
>>> >> >
>>> >> > On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
>>> >> > wrote:
>>> >> >>
>>> >> >> On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard
>>> >> >> <carlfeberhard@gmail.com>
>>> >> >> wrote:
>>> >> >> > I was incorrect in stating that the changes in the next
>>> >> >> > galaxy-dist
>>> >> >> > will
>>> >> >> > help in this case, unfortunately. From the stack trace you
>>> >> >> > posted,
>>> >> >> > there
>>> >> >> > is
>>> >> >> > a deeper error with your instance that the client-side changes
>>> >> >> > won't
>>> >> >> > help.
>>> >> >> >
>>> >> >> > Can you post the size, type, and name of the file you're trying
>>> >> >> > to
>>> >> >> > upload?
>>> >> >> >
>>> >> >>
>>> >> >> I can reproduce this by just typing "hello, world" into the
>>> >> >> "URL/Text:" box on the "Upload File" page. Any file of any type
>>> >> >> seems
>>> >> >> to trigger this problem.
>>> >> >>
>>> >> >> Thanks,
>>> >> >> Dan
>>> >> >>
>>> >> >>
>>> >> >> >
>>> >> >> > On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum
>>> >> >> > <dtenenba@fhcrc.org>
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard
>>> >> >> >> <carlfeberhard@gmail.com>
>>> >> >> >> wrote:
>>> >> >> >> > Another thing you might try is to upload the file to our test
>>> >> >> >> > server:
>>> >> >> >> > https://test.g2.bx.psu.edu/ and see if that works.
>>> >> >> >> >
>>> >> >> >>
>>> >> >> >> Thanks, that does work.
>>> >> >> >>
>>> >> >> >> Setting up an FTP server on my local installation seems pretty
>>> >> >> >> complex. All I really want to do is work around this issue and
>>> >> >> >> fool
>>> >> >> >> Galaxy into thinking that I have uploaded a file using the
>>> >> >> >> uploader...since this is a local installation I can put a file
>>> >> >> >> anywhere on my system, I don't have to actually upload it, just
>>> >> >> >> place
>>> >> >> >> it in a directory.
>>> >> >> >>
>>> >> >> >> If there is no such workaround, I'll wait for the fix, I guess.
>>> >> >> >> Thanks
>>> >> >> >> very much for working on this!
>>> >> >> >> Dan
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> >
>>> >> >> >> > On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard
>>> >> >> >> > <carlfeberhard@gmail.com>
>>> >> >> >> > wrote:
>>> >> >> >> >>
>>> >> >> >> >> If this is happening consistently and a refresh on the
>>> >> >> >> >> history
>>> >> >> >> >> isn't
>>> >> >> >> >> doing
>>> >> >> >> >> anything, you might try ftp upload:
>>> >> >> >> >> http://wiki.galaxyproject.org/FTPUpload
>>> >> >> >> >> or if you have permissions or are an admin you can try
>>> >> >> >> >> uploading
>>> >> >> >> >> to
>>> >> >> >> >> a
>>> >> >> >> >> data
>>> >> >> >> >> library:
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum
>>> >> >> >> >> <dtenenba@fhcrc.org>
>>> >> >> >> >> wrote:
>>> >> >> >> >>>
>>> >> >> >> >>> On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
>>> >> >> >> >>> <carlfeberhard@gmail.com>
>>> >> >> >> >>> wrote:
>>> >> >> >> >>> > What sort of database are you using on your local
>>> >> >> >> >>> > instance?
>>> >> >> >> >>> >
>>> >> >> >> >>>
>>> >> >> >> >>> The default (sqlite I guess). It's a completely vanilla
>>> >> >> >> >>> instance, I
>>> >> >> >> >>> have not touched the config files.
>>> >> >> >> >>> Dan
>>> >> >> >> >>>
>>> >> >> >> >>>
>>> >> >> >> >>> >
>>> >> >> >> >>> > On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum
>>> >> >> >> >>> > <dtenenba@fhcrc.org>
>>> >> >> >> >>> > wrote:
>>> >> >> >> >>> >>
>>> >> >> >> >>> >> On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
>>> >> >> >> >>> >> <carlfeberhard@gmail.com>
>>> >> >> >> >>> >> wrote:
>>> >> >> >> >>> >> > Thanks, Dan. That helps and I'll start looking into
>>> >> >> >> >>> >> > this.
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >> > We will be pushing out a new galaxy-dist revision
>>> >> >> >> >>> >> > sometime
>>> >> >> >> >>> >> > this
>>> >> >> >> >>> >> > week
>>> >> >> >> >>> >> > if
>>> >> >> >> >>> >> > all
>>> >> >> >> >>> >> > goes well. This revision includes some code for the
>>> >> >> >> >>> >> > history
>>> >> >> >> >>> >> > panel
>>> >> >> >> >>> >> > that
>>> >> >> >> >>> >> > may
>>> >> >> >> >>> >> > help handle this situation a bit better. I'd recommend
>>> >> >> >> >>> >> > updating
>>> >> >> >> >>> >> > to
>>> >> >> >> >>> >> > that
>>> >> >> >> >>> >> > revision when it comes out.
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >>
>>> >> >> >> >>> >> Thanks! Is there a workaround to upload a file or add it
>>> >> >> >> >>> >> to
>>> >> >> >> >>> >> my
>>> >> >> >> >>> >> history
>>> >> >> >> >>> >> in the meantime? Command-line is ok. If there isn't one,
>>> >> >> >> >>> >> that's
>>> >> >> >> >>> >> ok
>>> >> >> >> >>> >> too....
>>> >> >> >> >>> >> Dan
>>> >> >> >> >>> >>
>>> >> >> >> >>> >>
>>> >> >> >> >>> >>
>>> >> >> >> >>> >> > I'll let you know what I can find.
>>> >> >> >> >>> >> > Carl
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >> > On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum
>>> >> >> >> >>> >> > <dtenenba@fhcrc.org>
>>> >> >> >> >>> >> > wrote:
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> Hi Carl,
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
>>> >> >> >> >>> >> >> <carlfeberhard@gmail.com>
>>> >> >> >> >>> >> >> wrote:
>>> >> >> >> >>> >> >> > Heya, Dan.
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> > Sorry for the trouble.
>>> >> >> >> >>> >> >> > When you get that error again look for a line like
>>> >> >> >> >>> >> >> > you
>>> >> >> >> >>> >> >> > have
>>> >> >> >> >>> >> >> > above:
>>> >> >> >> >>> >> >> > Debug at:
>>> >> >> >> >>> >> >> > http://localhost:8080/_debug/view/1358978130
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> > If you open a new tab or window in your browser and
>>> >> >> >> >>> >> >> > go
>>> >> >> >> >>> >> >> > to
>>> >> >> >> >>> >> >> > the
>>> >> >> >> >>> >> >> > address
>>> >> >> >> >>> >> >> > ('http://localhost:8080/_debug ...'), you should see
>>> >> >> >> >>> >> >> > a
>>> >> >> >> >>> >> >> > more
>>> >> >> >> >>> >> >> > informative
>>> >> >> >> >>> >> >> > error message - complete with a list of function
>>> >> >> >> >>> >> >> > calls
>>> >> >> >> >>> >> >> > that
>>> >> >> >> >>> >> >> > led
>>> >> >> >> >>> >> >> > to
>>> >> >> >> >>> >> >> > the
>>> >> >> >> >>> >> >> > error
>>> >> >> >> >>> >> >> > (a stack trace).
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> > Can you post that stack trace when you see it?
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> Thanks for the quick response. Here it is:
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> URL:
>>> >> >> >> >>> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
>>> >> >> >> >>> >> >> line 364 in respond
>>> >> >> >> >>> >> >> app_iter = self.application(environ,
>>> >> >> >> >>> >> >> detect_start_response)
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
>>> >> >> >> >>> >> >> line 98 in __call__
>>> >> >> >> >>> >> >> environ, self.app)
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
>>> >> >> >> >>> >> >> line 539 in intercept_output
>>> >> >> >> >>> >> >> app_iter = application(environ,
>>> >> >> >> >>> >> >> replacement_start_response)
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
>>> >> >> >> >>> >> >> line 80 in __call__
>>> >> >> >> >>> >> >> return self.application(environ, start_response)
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
>>> >> >> >> >>> >> >> line 632 in __call__
>>> >> >> >> >>> >> >> return self.application(environ, start_response)
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py',
>>> >> >> >> >>> >> >> line 160 in __call__
>>> >> >> >> >>> >> >> body = method( trans, **kwargs )
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>>> >> >> >> >>> >> >> line 73 in decorator
>>> >> >> >> >>> >> >> return simplejson.dumps( func( self, trans, *args,
>>> >> >> >> >>> >> >> **kwargs
>>> >> >> >> >>> >> >> )
>>> >> >> >> >>> >> >> )
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>>> >> >> >> >>> >> >> line 317 in upload_async_create
>>> >> >> >> >>> >> >> datasets.append( create_dataset( name ) )
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
>>> >> >> >> >>> >> >> line 287 in create_dataset
>>> >> >> >> >>> >> >> return upload_common.new_upload( trans, cntrller,
>>> >> >> >> >>> >> >> ud,
>>> >> >> >> >>> >> >> library_bunch=library_bunch,
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD
>>> >> >> >> >>> >> >> )
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py',
>>> >> >> >> >>> >> >> line 213 in new_upload
>>> >> >> >> >>> >> >> return new_history_upload( trans, uploaded_dataset,
>>> >> >> >> >>> >> >> state )
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py',
>>> >> >> >> >>> >> >> line 118 in new_history_upload
>>> >> >> >> >>> >> >> hda.state = state
>>> >> >> >> >>> >> >> File
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/model/__init__.py',
>>> >> >> >> >>> >> >> line 1048 in set_dataset_state
>>> >> >> >> >>> >> >> object_session( self ).add( self.dataset )
>>> >> >> >> >>> >> >> AttributeError: 'NoneType' object has no attribute
>>> >> >> >> >>> >> >> 'add'
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> Dan
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >>
>>> >> >> >> >>> >> >> > We can take it from there and thanks,
>>> >> >> >> >>> >> >> > Carl
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> > On Wed, Jan 23, 2013 at 5:04 PM, Dan Tenenbaum
>>> >> >> >> >>> >> >> > <dtenenba@fhcrc.org>
>>> >> >> >> >>> >> >> > wrote:
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> Hi,
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> I installed galaxy completely from scratch:
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> rm -rf galaxy-dist && hg clone
>>> >> >> >> >>> >> >> >> https://bitbucket.org/galaxy/galaxy-dist/
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> I'm not a mercurial expert but I think I have
>>> >> >> >> >>> >> >> >> changeset
>>> >> >> >> >>> >> >> >> 8530:a4113cc1cb5e; at least that's the first entry
>>> >> >> >> >>> >> >> >> in
>>> >> >> >> >>> >> >> >> "hg
>>> >> >> >> >>> >> >> >> log".
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> Then started galaxy like this:
>>> >> >> >> >>> >> >> >> cd galaxy-dist
>>> >> >> >> >>> >> >> >> ./run.sh
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> I went to http://localhost:8080 and tried to upload
>>> >> >> >> >>> >> >> >> a
>>> >> >> >> >>> >> >> >> file. I
>>> >> >> >> >>> >> >> >> never
>>> >> >> >> >>> >> >> >> saw the file in my history, and this is what
>>> >> >> >> >>> >> >> >> printed
>>> >> >> >> >>> >> >> >> out
>>> >> >> >> >>> >> >> >> in
>>> >> >> >> >>> >> >> >> the
>>> >> >> >> >>> >> >> >> console after I clicked "Execute" on the "Upload
>>> >> >> >> >>> >> >> >> File"
>>> >> >> >> >>> >> >> >> page:
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574
>>> >> >> >> >>> >> >> >> Error:
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> request
>>> >> >> >> >>> >> >> >> returned None from get_history():
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create
>>> >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "POST
>>> >> >> >> >>> >> >> >> /tool_runner/upload_async_create HTTP/1.1" 500 -
>>> >> >> >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh;
>>> >> >> >> >>> >> >> >> Intel
>>> >> >> >> >>> >> >> >> Mac
>>> >> >> >> >>> >> >> >> OS X
>>> >> >> >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)
>>> >> >> >> >>> >> >> >> Chrome/24.0.1312.56
>>> >> >> >> >>> >> >> >> Safari/537.17"
>>> >> >> >> >>> >> >> >> Debug at:
>>> >> >> >> >>> >> >> >> http://localhost:8080/_debug/view/1358978130
>>> >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET
>>> >> >> >> >>> >> >> >> /tool_runner/upload_async_message HTTP/1.1" 200 -
>>> >> >> >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh;
>>> >> >> >> >>> >> >> >> Intel
>>> >> >> >> >>> >> >> >> Mac
>>> >> >> >> >>> >> >> >> OS X
>>> >> >> >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)
>>> >> >> >> >>> >> >> >> Chrome/24.0.1312.56
>>> >> >> >> >>> >> >> >> Safari/537.17"
>>> >> >> >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET
>>> >> >> >> >>> >> >> >> /history
>>> >> >> >> >>> >> >> >> HTTP/1.1"
>>> >> >> >> >>> >> >> >> 200
>>> >> >> >> >>> >> >> >> -
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> "http://localhost:8080/tool_runner/upload_async_message"
>>> >> >> >> >>> >> >> >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2)
>>> >> >> >> >>> >> >> >> AppleWebKit/537.17
>>> >> >> >> >>> >> >> >> (KHTML, like Gecko) Chrome/24.0.1312.56
>>> >> >> >> >>> >> >> >> Safari/537.17"
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> Hope someone can help.
>>> >> >> >> >>> >> >> >> Thanks,
>>> >> >> >> >>> >> >> >> Dan
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> ___________________________________________________________
>>> >> >> >> >>> >> >> >> Please keep all replies on the list by using "reply
>>> >> >> >> >>> >> >> >> all"
>>> >> >> >> >>> >> >> >> in your mail client. To manage your subscriptions
>>> >> >> >> >>> >> >> >> to
>>> >> >> >> >>> >> >> >> this
>>> >> >> >> >>> >> >> >> and other Galaxy lists, please use the interface
>>> >> >> >> >>> >> >> >> at:
>>> >> >> >> >>> >> >> >>
>>> >> >> >> >>> >> >> >> http://lists.bx.psu.edu/
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >> >
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >> >
>>> >> >> >> >>> >
>>> >> >> >> >>> >
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >
>>> >> >
>>> >
>>> >
>>
>>
>