Cloud Launch - Where is /mnt/galaxyData
Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected. -Dannon On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks. I was wrong before. I actually do see a /mnt/galaxyData. Should I not being seeing that? Am I not on cloudman 2.0? -Greg On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly. If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff. On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Here's what I'm seeing: ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
And is this a new instance you've just launched? If so, how'd you launch it? On Fri, Dec 20, 2013 at 2:37 PM, greg <margeemail@gmail.com> wrote:
Here's what I'm seeing:
ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your
single
persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunchand chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Yes, I just launched it a few hours ago. I just went here and filled out the form: https://usegalaxy.org/cloudlaunch I chose "data cluster" when prompted and enter 5GB. On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
And is this a new instance you've just launched? If so, how'd you launch it?
On Fri, Dec 20, 2013 at 2:37 PM, greg <margeemail@gmail.com> wrote:
Here's what I'm seeing:
ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted.
Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData
Background:
Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Just following up on this. So it's ok to do all of my customizations in /mnt/galaxyData? Or am I doing something wrong, and I need to figure out how to boot up into a version that has /mnt/galaxy? Thanks again, Greg On Fri, Dec 20, 2013 at 2:49 PM, greg <margeemail@gmail.com> wrote:
Yes, I just launched it a few hours ago.
I just went here and filled out the form: https://usegalaxy.org/cloudlaunch
I chose "data cluster" when prompted and enter 5GB.
On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
And is this a new instance you've just launched? If so, how'd you launch it?
On Fri, Dec 20, 2013 at 2:37 PM, greg <margeemail@gmail.com> wrote:
Here's what I'm seeing:
ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected.
-Dannon
On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote: > > Hi guys, > > I just launched an instance from https://usegalaxy.org/cloudlaunch > and > chose "data cluster" when prompted. > > Everything seems to have gone ok, but when I ssh in, I don't see > /mnt/galaxyData > > > Background: > > Basically we have a bioinformatics tool that needs SGE to run. So I > want to install it on a galaxy cloud instance and then provide the > share string to other researchers. > > I did this successfully a year or two ago by installing it to > /mnt/galaxyData. > > Thanks, > > Greg > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
Hey Greg, Sorry about the delay on this over the holidays. I see what you're working with now. If you install your customizations in a portable manner in /mnt/galaxyData that should be safe and we'll make sure to provide a smooth migration path going forward should that change. Only 'galaxy' type clusters will have /mnt/galaxy and data only clusters should continue to work just fine with /mnt/galaxyData. -Dannon On Mon, Dec 30, 2013 at 1:33 PM, greg <margeemail@gmail.com> wrote:
Just following up on this. So it's ok to do all of my customizations in /mnt/galaxyData?
Or am I doing something wrong, and I need to figure out how to boot up into a version that has /mnt/galaxy?
Thanks again,
Greg
Yes, I just launched it a few hours ago.
I just went here and filled out the form: https://usegalaxy.org/cloudlaunch
I chose "data cluster" when prompted and enter 5GB.
On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
And is this a new instance you've just launched? If so, how'd you launch it?
On Fri, Dec 20, 2013 at 2:37 PM, greg <margeemail@gmail.com> wrote:
Here's what I'm seeing:
ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either
empty
or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker <
dannon.baker@gmail.com>
wrote: > With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes > have > been merged to a single 'galaxy' volume. /mnt/galaxy is now your > single > persistent (by default, at least) volume, so, if you install your > tool > to > here and share everything should work as expected. > > -Dannon > > > On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> wrote: >> >> Hi guys, >> >> I just launched an instance from https://usegalaxy.org/cloudlaunch >> and >> chose "data cluster" when prompted. >> >> Everything seems to have gone ok, but when I ssh in, I don't see >> /mnt/galaxyData >> >> >> Background: >> >> Basically we have a bioinformatics tool that needs SGE to run. So I >> want to install it on a galaxy cloud instance and then provide
On Fri, Dec 20, 2013 at 2:49 PM, greg <margeemail@gmail.com> wrote: the
>> share string to other researchers. >> >> I did this successfully a year or two ago by installing it to >> /mnt/galaxyData. >> >> Thanks, >> >> Greg >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >
Perfect thanks! On Mon, Jan 6, 2014 at 1:16 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Greg,
Sorry about the delay on this over the holidays. I see what you're working with now. If you install your customizations in a portable manner in /mnt/galaxyData that should be safe and we'll make sure to provide a smooth migration path going forward should that change. Only 'galaxy' type clusters will have /mnt/galaxy and data only clusters should continue to work just fine with /mnt/galaxyData.
-Dannon
On Mon, Dec 30, 2013 at 1:33 PM, greg <margeemail@gmail.com> wrote:
Just following up on this. So it's ok to do all of my customizations in /mnt/galaxyData?
Or am I doing something wrong, and I need to figure out how to boot up into a version that has /mnt/galaxy?
Thanks again,
Greg
On Fri, Dec 20, 2013 at 2:49 PM, greg <margeemail@gmail.com> wrote:
Yes, I just launched it a few hours ago.
I just went here and filled out the form: https://usegalaxy.org/cloudlaunch
I chose "data cluster" when prompted and enter 5GB.
On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
And is this a new instance you've just launched? If so, how'd you launch it?
On Fri, Dec 20, 2013 at 2:37 PM, greg <margeemail@gmail.com> wrote:
Here's what I'm seeing:
ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly.
If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg <margeemail@gmail.com> wrote: > > Thanks. I was wrong before. I actually do see a /mnt/galaxyData. > > Should I not being seeing that? Am I not on cloudman 2.0? > > -Greg > > On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker > <dannon.baker@gmail.com> > wrote: > > With the Cloudman 2.0 release, the galaxyData and galaxyTools > > volumes > > have > > been merged to a single 'galaxy' volume. /mnt/galaxy is now your > > single > > persistent (by default, at least) volume, so, if you install your > > tool > > to > > here and share everything should work as expected. > > > > -Dannon > > > > > > On Fri, Dec 20, 2013 at 1:53 PM, greg <margeemail@gmail.com> > > wrote: > >> > >> Hi guys, > >> > >> I just launched an instance from > >> https://usegalaxy.org/cloudlaunch > >> and > >> chose "data cluster" when prompted. > >> > >> Everything seems to have gone ok, but when I ssh in, I don't see > >> /mnt/galaxyData > >> > >> > >> Background: > >> > >> Basically we have a bioinformatics tool that needs SGE to run. > >> So I > >> want to install it on a galaxy cloud instance and then provide > >> the > >> share string to other researchers. > >> > >> I did this successfully a year or two ago by installing it to > >> /mnt/galaxyData. > >> > >> Thanks, > >> > >> Greg > >> ___________________________________________________________ > >> 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/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > > > >
participants (2)
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Dannon Baker
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greg