testing updates on Galaxy CloudMan
I am at step 2 of Galaxy CloudMan deployment. "Now, manipulate Galaxy as desired." How do I test that my updates are working before proceeding to step 3? I assumed I could just type 'run.sh'. This starts Galaxy but: - fasta files do not display in the middle pane - png images generated by e.g. boxplot do not display in the middle pane - saving images does not work (get empty file) I need to know how people are customizing their cloud instance of galaxy. If it is NOT possible to test modifications in the usual way PLEASE would somebody simply confirm? I really would appreciate a response. Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113
Hi Isabelle, There is nothing special on the instance of Galaxy deployed through CloudMan, so any changes performed to the configuration of Galaxy should be tested the same way they would be tested if they were installed on a local system. That said, if there are system dependencies that need to be satisfied for some of the functionality to work, the update is more complicated because it would, most likely, involve creation of a new AMI. Especially if the mentioned functionality is not working on the default instance of CloudMan, we should work out the issue and release a new CloudMan AMI that fixes the underlying problem. I'll test the functionality you mentioned on a new instance of Galaxy CloudMan and help you resolving the issues. Enis On Fri, Mar 11, 2011 at 5:32 PM, Isabelle Phan < isabelle.phan@seattlebiomed.org> wrote:
I am at step 2 of Galaxy CloudMan deployment. "Now, manipulate Galaxy as desired."
How do I test that my updates are working before proceeding to step 3?
I assumed I could just type 'run.sh'. This starts Galaxy but: - fasta files do not display in the middle pane - png images generated by e.g. boxplot do not display in the middle pane - saving images does not work (get empty file)
I need to know how people are customizing their cloud instance of galaxy. If it is NOT possible to test modifications in the usual way PLEASE would somebody simply confirm?
I really would appreciate a response.
Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113
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Hello Enis, Many thanks for your reply. I've made some progress: the middle pane view works if I start galaxy with --deamon. I have figured out that I can test modifying the tools xml files (e.g. adding options). Now I am having issues with not being able to unmount /mnt/galaxyTools (step 3). It keeps complaining that the device is busy. - I check first all my windows that I am not accessing that directory - "lsof" shows nginx processes running under user galaxy. I kill all of them. Still can't unmount. - tried force unmount. Still no luck. Any ideas? Isabelle
-----Original Message----- From: Enis Afgan [mailto:eafgan@emory.edu] Sent: Friday, March 11, 2011 4:42 PM To: Isabelle Phan Cc: galaxy-dev@lists.bx.psu.edu; Gowthaman Ramasamy Subject: Re: [galaxy-dev] testing updates on Galaxy CloudMan
Hi Isabelle, There is nothing special on the instance of Galaxy deployed through CloudMan, so any changes performed to the configuration of Galaxy should be tested the same way they would be tested if they were installed on a local system. That said, if there are system dependencies that need to be satisfied for some of the functionality to work, the update is more complicated because it would, most likely, involve creation of a new AMI. Especially if the mentioned functionality is not working on the default instance of CloudMan, we should work out the issue and release a new CloudMan AMI that fixes the underlying problem. I'll test the functionality you mentioned on a new instance of Galaxy CloudMan and help you resolving the issues.
Enis
On Fri, Mar 11, 2011 at 5:32 PM, Isabelle Phan <isabelle.phan@seattlebiomed.org> wrote:
I am at step 2 of Galaxy CloudMan deployment. "Now, manipulate Galaxy as desired."
How do I test that my updates are working before proceeding to step 3?
I assumed I could just type 'run.sh'. This starts Galaxy but: - fasta files do not display in the middle pane - png images generated by e.g. boxplot do not display in the middle pane - saving images does not work (get empty file)
I need to know how people are customizing their cloud instance of galaxy. If it is NOT possible to test modifications in the usual way PLEASE would somebody simply confirm?
I really would appreciate a response.
Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 <tel:%2B1%28206%29256%207113>
___________________________________________________________ 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:
Hi Isabelle, It is most likely the NFS that's blocking the unmount. If you edit the file /etc/exports to comment the reference to /mnt/galaxyTools and then restart the NFS server using the following command '/etc/init.d/nfs-kernel-server restart', you will hopefully be able to unmount without any trouble. Enis On Fri, Mar 11, 2011 at 8:39 PM, Isabelle Phan < isabelle.phan@seattlebiomed.org> wrote:
Hello Enis,
Many thanks for your reply. I've made some progress: the middle pane view works if I start galaxy with --deamon. I have figured out that I can test modifying the tools xml files (e.g. adding options).
Now I am having issues with not being able to unmount /mnt/galaxyTools (step 3). It keeps complaining that the device is busy. - I check first all my windows that I am not accessing that directory - "lsof" shows nginx processes running under user galaxy. I kill all of them. Still can't unmount. - tried force unmount. Still no luck.
Any ideas?
Isabelle
-----Original Message----- From: Enis Afgan [mailto:eafgan@emory.edu] Sent: Friday, March 11, 2011 4:42 PM To: Isabelle Phan Cc: galaxy-dev@lists.bx.psu.edu; Gowthaman Ramasamy Subject: Re: [galaxy-dev] testing updates on Galaxy CloudMan
Hi Isabelle, There is nothing special on the instance of Galaxy deployed through CloudMan, so any changes performed to the configuration of Galaxy should be tested the same way they would be tested if they were installed on a local system. That said, if there are system dependencies that need to be satisfied for some of the functionality to work, the update is more complicated because it would, most likely, involve creation of a new AMI. Especially if the mentioned functionality is not working on the default instance of CloudMan, we should work out the issue and release a new CloudMan AMI that fixes the underlying problem. I'll test the functionality you mentioned on a new instance of Galaxy CloudMan and help you resolving the issues.
Enis
On Fri, Mar 11, 2011 at 5:32 PM, Isabelle Phan < isabelle.phan@seattlebiomed.org> wrote:
I am at step 2 of Galaxy CloudMan deployment. "Now, manipulate Galaxy as desired."
How do I test that my updates are working before proceeding to step 3?
I assumed I could just type 'run.sh'. This starts Galaxy but: - fasta files do not display in the middle pane - png images generated by e.g. boxplot do not display in the middle pane - saving images does not work (get empty file)
I need to know how people are customizing their cloud instance of galaxy. If it is NOT possible to test modifications in the usual way PLEASE would somebody simply confirm?
I really would appreciate a response.
Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 <tel:%2B1%28206%29256%207113>
___________________________________________________________ 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:
participants (2)
-
Enis Afgan -
Isabelle Phan