Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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 > ubuntu@:/mnt/galaxyData/files/000/dataset_11.dat > . > (note the 'ubuntu@' before the 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, 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 >> :/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_.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, 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 >> ubuntu@> >> > 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, loo
Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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 ubuntu@:/mnt/galaxyData/files/000/dataset_11.dat . (note the 'ubuntu@' before the 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, 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 > :/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_.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, 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 ubuntu@ >> > 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 ubuntu@ >> > public > >> > IP>:/mnt/galaxyData/files/000/dataset_.dat . > >> > > >> > Let us know if none of this works, > >> > Enis > >> > >
Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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_.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, 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 ubuntu@ > 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 ubuntu@ > public > > IP>:/mnt/galaxyData/files/000/dataset_.dat . > > > > Let us know if none of this works, > > Enis > > > > > > On Mon, Mar 28, 2011 at 12:02 PM, 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 > >> loc
Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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 ubuntu@ 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 ubuntu@ public > IP>:/mnt/galaxyData/files/000/dataset_.dat . > > Let us know if none of this works, > Enis > > > On Mon, Mar 28, 2011 at 12:02 PM, 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/ >> > ___ 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/
Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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 ubuntu@ [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 ubuntu@:/mnt/galaxyData/files/000/dataset_.dat . Let us know if none of this works, Enis On Mon, Mar 28, 2011 at 12:02 PM, 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/ > ___ 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/
Re: [galaxy-user] server error trying to DL data from galaxy on cloud
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/
