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, karlerhard@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, karlerhard@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, karlerhard@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:
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, karlerhard@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, karlerhard@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, karlerhard@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:
galaxy-user@lists.galaxyproject.org
-
Enis Afgan -
karlerhard＠berkeley.edu