Runtime on public Galaxy and current version of Galaxy on the Cloud?
Hi, I am finding that the run time on the public galaxy is exceptionally long, with job submitted yesterday still waiting to start. Given that I need to have analyses performed more quickly, I have tried to use Galaxy on the Cloud. Is this the following still the current version of cloudman to use? Current AMI: AMI: ami-da58aab3 Name: 861460482541/galaxy-cloudman-2011-03-22 I have set up instances for this version and have waited for over an hour for them to load, with multiple attempts to get the websites to open. All status indicators say that the instance is running. Any insight welcomed--- thanks--- Diana ********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802 email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895
Hi Diana, What type if instance did you use? You should use at least Large instace type. And did you make sure to format the user data as described in the wiki (http://wiki.g2.bx.psu.edu/CloudMan, under Step 2)? An alternative approach (which, granted, has not been publicized much yet) is to use http://bioCloudCentral.org and start your instance via that portal. I just tested it and and instance with Galaxy configured and running was up in about 5 minutes. When filling out the form, you may want to choose the Galaxy AMI (vs. the default CloudBioLinux one - which will also work) by clicking on the Advanced Options and choosing Galaxy Cloud AMI from the drop down menu). Let us know if you still have trouble, Enis On Sat, May 19, 2012 at 6:34 AM, Diana Cox-Foster <dxc12@psu.edu> wrote:
Hi, I am finding that the run time on the public galaxy is exceptionally long, with job submitted yesterday still waiting to start.
Given that I need to have analyses performed more quickly, I have tried to use Galaxy on the Cloud. Is this the following still the current version of cloudman to use?
*Current AMI:*
- AMI: ami-da58aab3 - Name: 861460482541/galaxy-cloudman-2011-03-22
I have set up instances for this version and have waited for over an hour for them to load, with multiple attempts to get the websites to open. All status indicators say that the instance is running.
Any insight welcomed--- thanks--- Diana
********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg
MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802
email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895
___________________________________________________________ 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:
Hi, I need some guidance on how to upload data files onto an instance of Galaxy on the Cloud. I have successfully established the instance, but am unable to ftp data sets into it. I have tried using my logon password for the instance to be able to gain access, without success. Is there a direct way to move data files from the public galaxy over to the instance without downloading the files onto my computer. Thanks for any help--- Diana ********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802 email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895 On May 18, 2012, at 5:54 PM, Enis Afgan wrote:
Hi Diana, What type if instance did you use? You should use at least Large instace type. And did you make sure to format the user data as described in the wiki (http://wiki.g2.bx.psu.edu/CloudMan, under Step 2)?
An alternative approach (which, granted, has not been publicized much yet) is to use http://bioCloudCentral.org and start your instance via that portal. I just tested it and and instance with Galaxy configured and running was up in about 5 minutes. When filling out the form, you may want to choose the Galaxy AMI (vs. the default CloudBioLinux one - which will also work) by clicking on the Advanced Options and choosing Galaxy Cloud AMI from the drop down menu).
Let us know if you still have trouble, Enis
On Sat, May 19, 2012 at 6:34 AM, Diana Cox-Foster <dxc12@psu.edu> wrote: Hi, I am finding that the run time on the public galaxy is exceptionally long, with job submitted yesterday still waiting to start.
Given that I need to have analyses performed more quickly, I have tried to use Galaxy on the Cloud. Is this the following still the current version of cloudman to use?
Current AMI:
AMI: ami-da58aab3 Name: 861460482541/galaxy-cloudman-2011-03-22 I have set up instances for this version and have waited for over an hour for them to load, with multiple attempts to get the websites to open. All status indicators say that the instance is running.
Any insight welcomed--- thanks--- Diana
********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg
MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802
email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895
___________________________________________________________ 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:
Hi Diana, How did you start your instance? What AMI is it based on? Attached is a screenshot of how I transfered a (random) file to an instance based on AMI ami-da58aab3. All I did before hand is register a new account within Galaxy and opened up an ftp connection. As far as transfering the data without having to download it to a local instance first, if the data has a publicly readable URL, you can simply paste it into Galax's URL/Text box under Get Data -> Upload File tool and the 3rd party transfer will automatically happen. Hope this helps, Enis On Fri, May 25, 2012 at 7:18 AM, Diana Cox-Foster <dxc12@psu.edu> wrote:
Hi, I need some guidance on how to upload data files onto an instance of Galaxy on the Cloud. I have successfully established the instance, but am unable to ftp data sets into it. I have tried using my logon password for the instance to be able to gain access, without success.
Is there a direct way to move data files from the public galaxy over to the instance without downloading the files onto my computer.
Thanks for any help--- Diana
********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg
MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802
email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895
On May 18, 2012, at 5:54 PM, Enis Afgan wrote:
Hi Diana, What type if instance did you use? You should use at least Large instace type. And did you make sure to format the user data as described in the wiki (http://wiki.g2.bx.psu.edu/CloudMan, under Step 2)?
An alternative approach (which, granted, has not been publicized much yet) is to use http://bioCloudCentral.org and start your instance via that portal. I just tested it and and instance with Galaxy configured and running was up in about 5 minutes. When filling out the form, you may want to choose the Galaxy AMI (vs. the default CloudBioLinux one - which will also work) by clicking on the Advanced Options and choosing Galaxy Cloud AMI from the drop down menu).
Let us know if you still have trouble, Enis
On Sat, May 19, 2012 at 6:34 AM, Diana Cox-Foster <dxc12@psu.edu> wrote:
Hi, I am finding that the run time on the public galaxy is exceptionally long, with job submitted yesterday still waiting to start.
Given that I need to have analyses performed more quickly, I have tried to use Galaxy on the Cloud. Is this the following still the current version of cloudman to use?
*Current AMI:*
- AMI: ami-da58aab3 - Name: 861460482541/galaxy-cloudman-2011-03-22
I have set up instances for this version and have waited for over an hour for them to load, with multiple attempts to get the websites to open. All status indicators say that the instance is running.
Any insight welcomed--- thanks--- Diana
********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg
MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802
email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895
___________________________________________________________ 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:
participants (2)
-
Diana Cox-Foster -
Enis Afgan