Excellent, it was the trailing dot that I was missing!

Thanks so much for the help, I will most certainly be using Galaxy again,
it's been very useful so far.

karl


> You're almost there, the command should be executed from your local
> machine
> (home directory is fine) and it should look as follows:
> scp -i <path to keyfile>
> ubuntu@<publicDNS>:/mnt/galaxyData/files/000/dataset_11.dat
> .
> (note the 'ubuntu@' before the <public DNS> and a trailing dot (.) - the
> dot
> means your current directory on your current machine, i.e., your home dir
> if
> that's where you are executing the command from)
>
> I apologize for the trouble in getting the this data out and hope it does
> not keep you from using Galaxy Cloud in the future (we're looking into why
> the browser-based data copy didn't work and should have a fix shortly for
> the main app).
>
> Enis
>
> On Mon, Mar 28, 2011 at 6:16 PM, <karlerh...@berkeley.edu> wrote:
>
>>
>> Hi Enis
>>
>> I'm getting the following error at the bottom of the galaxy log:
>>
>> RuntimeError: Content returned before start_response called
>>
>> I have no idea how to fix this, but I'm trying to focus now on actually
>> getting the files, as I don't really need this galaxy instance anymore.
>> I
>> have been able to locate where my files are and which are the ones I
>> want.
>>
>> I've tried the following command:
>>
>> scp -i <path to keyfile>
>> <publicDNS>:/mnt/galaxyData/files/000/dataset_11.dat
>>
>> But I just get the scp usage statement coming back.  Is there something
>> else I'm missing here?  I was executing this command in my home
>> directory,
>> do I need to be somewhere else?  I feel like I'm so close!!!
>>
>> Thanks so much for your help so far, I'd be lost otherwise.
>>
>> karl
>>
>>
>>
>>
>>
>> > Hi Karl,
>> > Hmm, not having Galaxy accessible is definitely not a step in the
>> right
>> > direction.
>> > Being signed into command line is not an issue; something else must
>> have
>> > gone wrong. To start, please take a look at the (bottom of) galaxy log
>> > file
>> > (and email the relevant part if you don't see how to fix it
>> immediately);
>> > the file is saved as /mnt/galaxyTools/galaxy-central/paster.log
>> >
>> > As far as the location of the files in data libraries, they should be
>> > stored
>> > in the same location as history datasets, namely
>> > /mnt/galaxyData/files/000/dataset_<ID>.dat
>> > Because all of the datasets are named simply based on the database ID,
>> it
>> > won't necessarily be obvious which file to get without doing some
>> (python)
>> > coding or doing some guess work. If you know how large your files is,
>> you
>> > can easily narrow your choices down by listing the contents of the
>> given
>> > directory and sorting it by size (using command ls -lS), then pulling
>> out
>> > the file(s) that you want. If several files are of approx. the same
>> size,
>> > open them up and see which one you want.
>> >
>> > Good luck and let us know if you have any more trouble,
>> > Enis
>> >
>> >
>> > On Mon, Mar 28, 2011 at 3:35 PM, <karlerh...@berkeley.edu> wrote:
>> >
>> >>
>> >> Hello Enis,
>> >>
>> >> Thanks for the quick response and suggestions.  I actually did have a
>> >> job
>> >> running while I tried to download a file the first time, that's the
>> >> first
>> >> time it gave the error message.  But the jobs have long since
>> finished
>> >> and
>> >> it's still giving the error message.
>> >>
>> >> I've been able to edit the universe_wsgi.ini file to "debug = False",
>> >> but
>> >> now I'm getting an "Internal server error" when I try to reload the
>> >> galaxy
>> >> instance.  Should I be signed out at the command-line to reload
>> galaxy
>> >> from a browser?  Forgive my simplicity, I'm really not at all
>> >> command-line
>> >> savvy.
>> >>
>> >> Also, another extremely basic problem I have is I just don't know
>> where
>> >> the data library that holds my files is located.  Any help would be
>> >> greatly appreciated.
>> >>
>> >> best,
>> >>
>> >> karl
>> >>
>> >>
>> >> > Hi Karl,
>> >> > As you see from the error message, you seem to be getting this
>> error
>> >> > because
>> >> > the machine is running out of memory. This can in part be caused by
>> a
>> >> > configuration option that might be set in Galaxy's
>> universe_wsgi.ini
>> >> file
>> >> > (see below).
>> >> > Did you have any jobs running while trying to download the file?
>> >> Waiting
>> >> > until those finish might free up some memory.
>> >> >
>> >> > A thing to try is to connect to the instance, edit Galaxy's
>> >> > universe_wsgi.ini file to se debug = False, restart Galaxy and try
>> >> > again. Are you familiar with that at all?
>> >> > The basic steps are as follows:
>> >> > [local]$ ssh -i <path to your AWS private key file>
>> ubuntu@<instance
>> >> > public
>> >> > IP>
>> >> > [ec2]$ sudo su galaxy
>> >> > [ec2]$ cd /mnt/galaxyTools/galaxy-central
>> >> > [ec2]$ vi universe_wsgi.ini  -- edit file (around line 226) to set:
>> >> debug
>> >> > =
>> >> > False
>> >> > [ec2]$ sh run.sh --stop-daemon
>> >> > [ec2]$ sh run.sh --daemon
>> >> >
>> >> > Yet another option is to connect the instance in the same way, look
>> >> > through
>> >> > the data library on the file system and manually copy the file out
>> of
>> >> the
>> >> > instance. You can use the following command to copy the file to
>> your
>> >> local
>> >> > instance:
>> >> > [local]$ scp -i <path to your AWS private key file>
>> ubuntu@<instance
>> >> > public
>> >> > IP>:/mnt/galaxyData/files/000/dataset_<ID>.dat .
>> >> >
>> >> > Let us know if none of this works,
>> >> > Enis
>> >> >
>> >> >
>> >> > On Mon, Mar 28, 2011 at 12:02 PM, <karlerh...@berkeley.edu> wrote:
>> >> >
>> >> >>
>> >> >> Hello,
>> >> >>
>> >> >> I'm trying to download the library files I processed on my galaxy
>> >> cloud
>> >> >> instance, but I'm getting an error.  At the top (on the right
>> panel)
>> >> it
>> >> >> says "Server Error" and then lists the URL where the data should
>> be
>> >> and
>> >> >> then lists:
>> >> >>
>> >> >> Module paste.exceptions.errormiddleware:143 in __call__
>> >> >> <<          try:
>> >> >>                __traceback_supplement__ = Supplement, self,
>> environ
>> >> >>                app_iter = self.application(environ,
>> start_response)
>> >> >>                return self.make_catching_iter(app_iter, environ)
>> >> >>            except:>>  app_iter = self.application(environ,
>> >> >> start_response)
>> >> >> Module paste.debug.prints:98 in __call__
>> >> >> <<          try:
>> >> >>                status, headers, body = wsgilib.intercept_output(
>> >> >>                    environ, self.app)
>> >> >>                if status is None:
>> >> >>                    # Some error occurred>>  environ, self.app)
>> >> >> Module paste.wsgilib:544 in intercept_output
>> >> >> <<      try:
>> >> >>            for item in app_iter:
>> >> >>                output.write(item)
>> >> >>        finally:
>> >> >>            if hasattr(app_iter, 'close'):>>  output.write(item)
>> >> >> MemoryError: out of memory
>> >> >>
>> >> >>
>> >> >>
>> >> >> Is there some easy fix to this?  I'd really like to get that data
>> off
>> >> of
>> >> >> the cloud instance and be able to terminate it.
>> >> >>
>> >> >> thanks,
>> >> >>
>> >> >> karl
>> >> >>
>> >> >> ___________________________________________________________
>> >> >> The Galaxy User list should be used for the discussion of
>> >> >> Galaxy analysis and other features on the public server
>> >> >> at usegalaxy.org.  Please keep all replies on the list by
>> >> >> using "reply all" in your mail client.  For discussion of
>> >> >> local Galaxy instances and the Galaxy source code, please
>> >> >> use the Galaxy Development list:
>> >> >>
>> >> >>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>> >> >>
>> >> >> To manage your subscriptions to this and other Galaxy lists,
>> >> >> please use the interface at:
>> >> >>
>> >> >>  http://lists.bx.psu.edu/
>> >> >>
>> >> >
>> >>
>> >>
>> >>
>> >
>>
>>
>>
>


___________________________________________________________
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