[galaxy-user] Question on megablast databases
Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database? Many thanks, Kathryn ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] [External] Re: Question on megablast databases
Jen, Thank you very much for the information. They are very informative. I found the htgs and wgs databases information there. What does nt 28-Jan-2013 stand for? Meantime, if I am looking for virus containing database, I found wgs is one. Can anyone confirm or advice further if there is other options (database)? Thank you again! Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, May 24, 2013 3:36 PM To: Sun, Wenping [USA] Cc: galaxy-user@lists.bx.psu.edu Subject: [External] Re: [galaxy-user] Question on megablast databases Hi Kathryn, These first three are three different types of sequence databases available from GenBank The last is a genome assembly for the phiX174 genome. Information about all can be found here: http://www.ncbi.nlm.nih.gov/genbank/ There are many uses, one example is covered in our Metagenomics publication: https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter Thanks! Jen Galaxy team On 5/24/13 6:59 AM, Sun, Wenping [USA] wrote: Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database? Many thanks, Kathryn ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] [External] Re: Question on galaxy data visualization
Jen, Thanks for the information. Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Monday, May 13, 2013 6:18 PM To: Sun, Wenping [USA] Cc: galaxy-user@lists.bx.psu.edu Subject: [External] Re: [galaxy-user] Question on galaxy data visualization Hello Kathryn, Trackster is the primary data visualization tool and can be accessed by clicking on the mini graph icon within a dataset: [cid:image001.png@01CE50AA.D31EDA40] or by going to Visualization in the upper menu bar and starting a new track browser. http://wiki.galaxyproject.org/Learn#Visualization If you are interested, for certain datasets, the icon will also offer other options: Circster and/or Scatterplot. The tool group Graph/Display Data has graphing tools and tools that prepare data to be visualized. The tool group Motif Tools has a sequence logo generator, and the groups NGS: QC and manipulation and BEDTools have more graphing tools. Hopefully this helps, Jen Galaxy team On 5/13/13 11:08 AM, Sun, Wenping [USA] wrote: Dear galaxy group, I have question on the data visualization from output of galaxy pipeline. Is there any ideogram tool inside of galaxy? Regards, Kathryn ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org inline: image001.png___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] galaxy test dataset listing
Hello, It is good to see there are some testing dataset in fastq format from galaxy s3. Is there any brief information about the test data? For example, RNAseq or Chipseq, etc? Many thanks, Kathryn ___ 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] [External] Re: galaxy cloudman login
Thank you for the reply. When I check admin from cloudman interface, I still see myself as admin user. However, when I went to galaxy web to continue my work, I couldn't login( as error message below). I can re-register with the same user name/email, however, my history is empty. I already had much work processed previously. 1. how to retain my previous work? 2. I could not find Mange User under admin, either from cloudman and galaxy web. Where is it? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Wednesday, January 02, 2013 4:50 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login To be clear, your admin user still works on this instance but another one does not? If this is the case, can you log in as the admin user (and, if not, simply register a new user and make it an admin) and take a look at the user list in the admin panel? To get to the user list when in Galaxy, just click Admin at the top and then Manage Users. Are there users listed? If your user is listed but you're unable to log in, you can reset your password here. -Dannon On Dec 31, 2012, at 10:41 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Hello, I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1sttime restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all (error:no such user). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What's the issue with the log in?? It is taking time to repeat previous data/history. I need your help to retrieve my login. Thank you in advance, Kathryn ___ 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/
[galaxy-user] galaxy cloudman login
Hello, I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1st time restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all (error:no such user). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What's the issue with the log in?? It is taking time to repeat previous data/history. I need your help to retrieve my login. Thank you in advance, Kathryn ___ 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/
[galaxy-user] galaxy cluster nodes from the cloudlaunch site
Dear Galaxy users, I created galaxy instance using galaxy ami the first time. When I re-launch via cloudlaunch site the 2nd time, I have question on adding cluster nodes. There are several pull-down options for the nodes type, no matter which type I choose, they always generate nodes with only 15gb. Is there other option I can have option to define the root space for the nodes? Thank you, Kathryn ___ 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] [External] Re: galaxy cluster nodes from the cloudlaunch site
Thanks for the information. Would you help providing further information on
expanding ebs volume via cloudman UI?
Thank you in advance,
Kathryn
-Original Message-
From: dannonba...@me.com [mailto:dannonba...@me.com]
Sent: Thursday, December 27, 2012 10:03 AM
To: Sun, Wenping [USA]
Cc: galaxy-u...@bx.psu.edu
Subject: [External] Re: [galaxy-user] galaxy cluster nodes from the cloudlaunch
site
The root size for the worker nodes doesn't matter. The only thing relevant to
Galaxy here are the available compute units and memory.
The only storage and working space used is actually attached to the master node
(the EBS volume you configure at initial launch) and shared over NFS with the
workers. If you find yourself needing more space, you can expand this volume
through the cloudman UI if you want.
-Dannon
Sun, Wenping [USA] wrote:
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Dear Galaxy users,
I created galaxy instance using galaxy ami the first time. When I re- launch
via cloudlaunch site the 2nd time, I have question on adding cluster nodes.
There are several pull-down options for the nodes type, no matter which type I
choose, they always generate nodes with only 15gb. Is there other option I can
have option to define the root space for the nodes?
Thank you,
Kathryn
___
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] [External] Re: galaxy cluster nodes from the cloudlaunch site
Thank you for the help.
I assume that if galaxy will shutting down while re-sizing, the current running
jobs will be stopped. Could the running jobs be suspended which will be
continuing after auto-restart? If not, I may need to wait my job finished. It
will be very helpful if you can confirm this.
Additional question, is there any way that I can adjust root, ebs volumes while
initiating at cloudlaunch site? This would be help saving the time for the
re-sizing as you mentioned.
Thank you in advance,
Kathryn
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Thursday, December 27, 2012 10:22 AM
To: Sun, Wenping [USA]
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [External] Re: [galaxy-user] galaxy cluster nodes from the
cloudlaunch site
In the main (non-admin) cloudman UI you'll see a little icon next to the volume
size. Click this and you'll have the opportunity to enter a new size. Upon
submitting this, galaxy will need to temporarily shut down, but it should be
automatically restarted once the procedure is complete. Note that resizing can
take quite some time (hours, even) depending on the size of the EBS volume in
question.
On Dec 27, 2012, at 10:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
Thanks for the information. Would you help providing further information on
expanding ebs volume via cloudman UI?
Thank you in advance,
Kathryn
-Original Message-
From: dannonba...@me.com [mailto:dannonba...@me.com]
Sent: Thursday, December 27, 2012 10:03 AM
To: Sun, Wenping [USA]
Cc: galaxy-u...@bx.psu.edu
Subject: [External] Re: [galaxy-user] galaxy cluster nodes from the
cloudlaunch site
The root size for the worker nodes doesn't matter. The only thing relevant
to Galaxy here are the available compute units and memory.
The only storage and working space used is actually attached to the master
node (the EBS volume you configure at initial launch) and shared over NFS
with the workers. If you find yourself needing more space, you can expand
this volume through the cloudman UI if you want.
-Dannon
Sun, Wenping [USA] wrote:
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Dear Galaxy users,
I created galaxy instance using galaxy ami the first time. When I re- launch
via cloudlaunch site the 2nd time, I have question on adding cluster nodes.
There are several pull-down options for the nodes type, no matter which type
I choose, they always generate nodes with only 15gb. Is there other option I
can have option to define the root space for the nodes?
Thank you,
Kathryn
___
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] [External] Re: galaxy cluster nodes from the cloudlaunch site
Thanks for the answers. From a user side, it would be more flexible to initiate the master instance via aws site; or have the user be able to choose some major options if initiating from cloudlaunch site. I wonder either one would be the future concern for galaxy development. If so, I am looking forward to the capability. Thanks, Kathryn -Original Message- From: dannonba...@me.com [mailto:dannonba...@me.com] Sent: Thursday, December 27, 2012 10:35 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cluster nodes from the cloudlaunch site Correct, all running jobs will be stopped and there isn't currently any way to suspend running jobs. Jobs that haven't dispatched yet (not in the 'running' state) should, however, resume after the restart. And as far as resizing from cloudlaunch, no, currently resizing is only possible from a running cluster though this is an interesting idea. Sun, Wenping [USA] wrote: Thank you for the help. I assume that if galaxy will shutting down while re-sizing, the current running jobs will be stopped. Could the running jobs be suspended which will be continuing after auto-restart? If not, I may need to wait my job finished. It will be very helpful if you can confirm this. Additional question, is there any way that I can adjust root, ebs volumes while initiating at cloudlaunch site? This would be help saving the time for the re-sizing as you mentioned. Thank you in advance, Kathryn ___ 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] [External] Re: galaxy cluster nodes from the cloudlaunch site
Okay, sorry for the confusion. I meant that while initiating via aws, there are more options to choose the root and ebs volumes which it is very flexible. We do have the option to initiating the instance at the FIRST time via aws site (or from cloudlaunch site as you mentioned); whereas all the later launches have to go to cloudlaunch site. What I found was, the sizes that I initiated first at aws site were lost while relaunching from cloudlaunch. Moreover, it takes more time to re-size them. Hope this helps and thank you, Kathryn -Original Message- From: dannonba...@me.com [mailto:dannonba...@me.com] Sent: Thursday, December 27, 2012 10:51 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cluster nodes from the cloudlaunch site Sun, Wenping [USA] wrote: From a user side, it would be more flexible to initiate the master instance via aws site; or have the user be able to choose some major options if initiating from cloudlaunch site. I wonder either one would be the future concern for galaxy development. If so, I am looking forward to the capability. I'm not sure I understand, could you elaborate? Right now, all resizing (regardless of how you start the instance, via cloudlaunch or aws) requires you to use cloudman running on the instance. ___ 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] [External] Re: galaxy cluster nodes from the cloudlaunch site
Hello, I tried several time of re-sizing to create data volume as you indicated
below. However, there is nothing change, either from galaxy log and aws
console. Is there anything else that may miss from the your procedure below?
Thanks,
Kathryn
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Thursday, December 27, 2012 10:22 AM
To: Sun, Wenping [USA]
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [External] Re: [galaxy-user] galaxy cluster nodes from the
cloudlaunch site
In the main (non-admin) cloudman UI you'll see a little icon next to the volume
size. Click this and you'll have the opportunity to enter a new size. Upon
submitting this, galaxy will need to temporarily shut down, but it should be
automatically restarted once the procedure is complete. Note that resizing can
take quite some time (hours, even) depending on the size of the EBS volume in
question.
On Dec 27, 2012, at 10:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
Thanks for the information. Would you help providing further information on
expanding ebs volume via cloudman UI?
Thank you in advance,
Kathryn
-Original Message-
From: dannonba...@me.com [mailto:dannonba...@me.com]
Sent: Thursday, December 27, 2012 10:03 AM
To: Sun, Wenping [USA]
Cc: galaxy-u...@bx.psu.edu
Subject: [External] Re: [galaxy-user] galaxy cluster nodes from the
cloudlaunch site
The root size for the worker nodes doesn't matter. The only thing relevant
to Galaxy here are the available compute units and memory.
The only storage and working space used is actually attached to the master
node (the EBS volume you configure at initial launch) and shared over NFS
with the workers. If you find yourself needing more space, you can expand
this volume through the cloudman UI if you want.
-Dannon
Sun, Wenping [USA] wrote:
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Dear Galaxy users,
I created galaxy instance using galaxy ami the first time. When I re- launch
via cloudlaunch site the 2nd time, I have question on adding cluster nodes.
There are several pull-down options for the nodes type, no matter which type
I choose, they always generate nodes with only 15gb. Is there other option I
can have option to define the root space for the nodes?
Thank you,
Kathryn
___
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] [External] Re: galaxy cloudman login and aws instance
Thanks and my question is-- How to shutting down the cloud if working on main.g2.bx.psu.edu? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:38 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws instance It looks like you've worked on both the public galaxy site we provide (main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance won't be automatically migrated to the cloud instance and vice versa. All work done on the cloud site will remain there and persist after termination and restart of that cloud cluster. Work on main.g2.bx.psu.edu is completely separate and will remain there. -Dannon On Dec 20, 2012, at 12:44 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Dear galaxy members, I have question on galaxy running on cloud with the issue of authorization matter. I have launched aws galaxy cloudman instances to work with, shutting down the cluster afterwards. Then the 2nd time here are the steps that I did- 1. Launch the galaxy at cloudlaunch site 2. Register and then log in 3. Worked with data uploading and processing (the login information can see from pull-down menu), as well as the data history image001.jpg 4. Go to aws console to check, find the instance is running 5. Copy the dns site followed by /cloud to check the cluster nodes, click access galaxy button there 6. On the galaxy window choose user login 7. And here is the window I have - I cannot login and no history data there. image002.jpg My question: it seems that the two galaxy access is not the same. I rather to use the site from cloudlaunch site if it is preferred. However, I still have to go to the instance DNS site for shutting down the instance/cluster to avoid aws unnecessary charge. And, if I need to add cluster nodes, I still need to go to the DNS site. What is the appropriate procedure I need to follow to retain the data history and log in between two accesses, especially while shutting down and restart? I really appreciate your inputs and helps! Kind regards, Kathryn ___ 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] [External] Re: galaxy cloudman login and aws instance
Thanks. When I use main.g2.bx.psu.edu to access the galaxy, I did see the ec2 instance initiated from my aws console. Why this happen and what this instance doing? Meantime, what is the data security on main.g2.bx.psu.edu? If I use aws instance for the data works, do I have to terminate the ec2 instances/cluster and then launch the instance every time? Thank you, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:43 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cloudman login and aws instance Ahh, ok. If you want to work exclusively on main and don't have the need for a cloud instance, just terminate (and permanently delete, if desired) cloud instances through the cloudman interface and keep using main.g2.bx.psu.edu. -Dannon On Dec 20, 2012, at 1:41 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Thanks and my question is-- How to shutting down the cloud if working on main.g2.bx.psu.edu? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:38 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws instance It looks like you've worked on both the public galaxy site we provide (main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance won't be automatically migrated to the cloud instance and vice versa. All work done on the cloud site will remain there and persist after termination and restart of that cloud cluster. Work on main.g2.bx.psu.edu is completely separate and will remain there. -Dannon On Dec 20, 2012, at 12:44 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Dear galaxy members, I have question on galaxy running on cloud with the issue of authorization matter. I have launched aws galaxy cloudman instances to work with, shutting down the cluster afterwards. Then the 2nd time here are the steps that I did- 1. Launch the galaxy at cloudlaunch site 2. Register and then log in 3. Worked with data uploading and processing (the login information can see from pull-down menu), as well as the data history image001.jpg 4. Go to aws console to check, find the instance is running 5. Copy the dns site followed by /cloud to check the cluster nodes, click access galaxy button there 6. On the galaxy window choose user login 7. And here is the window I have - I cannot login and no history data there. image002.jpg My question: it seems that the two galaxy access is not the same. I rather to use the site from cloudlaunch site if it is preferred. However, I still have to go to the instance DNS site for shutting down the instance/cluster to avoid aws unnecessary charge. And, if I need to add cluster nodes, I still need to go to the DNS site. What is the appropriate procedure I need to follow to retain the data history and log in between two accesses, especially while shutting down and restart? I really appreciate your inputs and helps! Kind regards, Kathryn ___ 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] [External] Re: galaxy cloudman login and aws instance
Thank you very much for the information. For the last part of using ec2 instances at aws, is there an option that I can control galaxy's operation at aws site? This way I can start/stop the instance when I need. I am not willing to terminate the instance since everything will be lost. Meantime, I am wondering the data structure on ec2 galaxy instance. Where is the location for the data uploaded from the galaxy gui? If I ssh the Ubuntu, where is the data directory for holding the work? Thank you, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 2:23 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cloudman login and aws instance The ec2 instance is your personal instance that you have complete control over for customization, you don't have a personal quota, nobody else will be waiting in line to run jobs, etc. The server at main.g2.bx.psu.edu is our public galaxy instance that we provide and administer, but because it's a public service we do have quotas and sometimes processing queues, and so on. Regarding data security, here's the relevant snippet from the public galaxy welcome page: This is a free, public, internet accessible resource. Data transfer and data storage are not encrypted. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to any public site, including this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to setup your own local Galaxy instance or run Galaxy on the cloud. Lastly, for aws, you don't *have* to terminate the ec2 instance and start it back up when you want to use it, but remember that for every hour of use Amazon does bill you. If you aren't running any jobs on the instance, it would make sense to terminate it and start it back up when you want it again. On Dec 20, 2012, at 1:52 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Thanks. When I use main.g2.bx.psu.edu to access the galaxy, I did see the ec2 instance initiated from my aws console. Why this happen and what this instance doing? Meantime, what is the data security on main.g2.bx.psu.edu? If I use aws instance for the data works, do I have to terminate the ec2 instances/cluster and then launch the instance every time? Thank you, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:43 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cloudman login and aws instance Ahh, ok. If you want to work exclusively on main and don't have the need for a cloud instance, just terminate (and permanently delete, if desired) cloud instances through the cloudman interface and keep using main.g2.bx.psu.edu. -Dannon On Dec 20, 2012, at 1:41 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Thanks and my question is-- How to shutting down the cloud if working on main.g2.bx.psu.edu? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:38 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws instance It looks like you've worked on both the public galaxy site we provide (main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance won't be automatically migrated to the cloud instance and vice versa. All work done on the cloud site will remain there and persist after termination and restart of that cloud cluster. Work on main.g2.bx.psu.edu is completely separate and will remain there. -Dannon On Dec 20, 2012, at 12:44 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Dear galaxy members, I have question on galaxy running on cloud with the issue of authorization matter. I have launched aws galaxy cloudman instances to work with, shutting down the cluster afterwards. Then the 2nd time here are the steps that I did- 1. Launch the galaxy at cloudlaunch site 2. Register and then log in 3. Worked with data uploading and processing (the login information can see from pull-down menu), as well as the data history image001.jpg 4. Go to aws console to check, find the instance is running 5. Copy the dns site followed by /cloud to check the cluster nodes, click access galaxy button there 6. On the galaxy window choose user login 7. And here is the window I have - I cannot login and no history data there. image002.jpg My question: it seems that the two galaxy access is not the same. I rather to use the site from cloudlaunch site if it is preferred. However, I still have to go
Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance
We'd recommend you not ever stop/start through the aws console -- this is basically guaranteed to cause problems with your instance. Always use the cloudman interface (on your ec2 instance -- http://ec2_instance/cloud) to terminate, and then use usegalaxy.org/cloudlaunch to restart it. The problem is that if use usegalaxy.org/cloudlaunch to restart galaxy, it will launch to main.g2.bx.psu.edu, where I have no control on the data security and running queues. Meanwhile, the correspondingly initiated ec2 instance is brand new and has no previous work records to track with. In this is the case, it would be great that if galaxy cloudman can be designed more aws instance friendly in the future. Thank you, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 2:43 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: Re: [External] Re: [galaxy-user] galaxy cloudman login and aws instance On Dec 20, 2012, at 2:33 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Thank you very much for the information. For the last part of using ec2 instances at aws, is there an option that I can control galaxy's operation at aws site? This way I can start/stop the instance when I need. I am not willing to terminate the instance since everything will be lost. We'd recommend you not ever stop/start through the aws console -- this is basically guaranteed to cause problems with your instance. Always use the cloudman interface (on your ec2 instance -- http://ec2_instance/cloud) to terminate, and then use usegalaxy.org/cloudlaunch to restart it. Meantime, I am wondering the data structure on ec2 galaxy instance. Where is the location for the data uploaded from the galaxy gui? If I ssh the Ubuntu, where is the data directory for holding the work? Everything will be in /mnt/galaxyData/files (which is symlinked to /mnt/galaxyTools/galaxy-central/database/files). Note that the filenames will be by id (like files/000/dataset_001.dat is dataset id 1, etc), and not particularly accessible in this format without a little extra legwork. ___ 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/
[galaxy-user] question on galaxy reference genome window
Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down menu can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? If so, how? 2. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected Thank you very much for your inputs and helps! Kind regards, Kathryn ___ 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] [External] Re: question on galaxy reference genome window
Hi Dannon, Yes, you are correct! I installed galaxy from scratch on the cloud. I will check the site you provided and see how it goes. I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the galaxy web running again (the instance running however the DNS not able to access). What is the right steps to stop the instances and restart it next time? Thank you in advance, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Wednesday, December 19, 2012 10:27 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] question on galaxy reference genome window Kathryn, Are you using the galaxy cloud configuration provided by the team, or have you installed your own galaxy on a cloud instance? It sounds like the latter, in which case you'll need to configure reference as detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You may also want to experiment with using the preconfigured cloud instances, see this page for more information on those: http://wiki.galaxyproject.org/CloudMan -Dannon On Dec 18, 2012, at 2:21 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down menu can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? If so, how? 2. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected Thank you very much for your inputs and helps! Kind regards, Kathryn ___ 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/
[galaxy-user] upload workflow on cloudman
Dear galaxy users, I tried to follow the instruction to see how the workflow worked by using the one on the support site Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga However, it takes very very long time and remains the following state for several hours. Is this normal? I set up 100gb for cluster and added 4 nodes same as the demo. [cid:image001.jpg@01CDDDF2.58691C00] Thank you very much! Kathryn inline: image001.jpg___ 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/
