Initial configuration

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Initial configuration

matthew couchman (JIC)

Hi,

 

I’m installing WebApollo for the first time and I have a question regarding the Configure and Data Generation pages. The pages use /opt/apollo/ as a home for Apollo data but I’m not sure where to set this as the Apollo data directory. I’ve seen some references to a config.properties file but I can’t find that in my v2.0.2 download.

 

Thanks in advance for your help,

 

                                Matt.





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Re: Initial configuration

nathandunn

If you are installing 2.0.2 you set data per organism.  For example, if you had two organisms (e.g., cow and dog), you would might put your jbrowse data in a directory /opt/apollo/cow and /research/disk2/dog,  respectively.   

When creating the organism you would point to those directories, which would contain trackList.json and the seq directory . . as any jbrowse directory would.  


Nathan

On Apr 8, 2016, at 3:57 AM, matthew couchman (JIC) <[hidden email]> wrote:

Hi,
 
I’m installing WebApollo for the first time and I have a question regarding the Configure and Data Generation pages. The pages use /opt/apollo/ as a home for Apollo data but I’m not sure where to set this as the Apollo data directory. I’ve seen some references to a config.properties file but I can’t find that in my v2.0.2 download.
 
Thanks in advance for your help,
 
                                Matt.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





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RE: Initial configuration

matthew couchman (JIC)

Hi Nathan,

 

Thanks for your reply, that’s cleared that up though I have a further problem now: the text boxes are greyed out and show a no entry cursor when I mouse over them. The admin tab says “Problem loading admin page”. Do you know where I need to look to remedy this?

 

Many thanks,

 

                                Matt.

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Nathan Dunn
Sent: 08 April 2016 15:26
To: [hidden email]
Subject: Re: [apollo] Initial configuration

 

 

If you are installing 2.0.2 you set data per organism.  For example, if you had two organisms (e.g., cow and dog), you would might put your jbrowse data in a directory /opt/apollo/cow and /research/disk2/dog,  respectively.   

 

When creating the organism you would point to those directories, which would contain trackList.json and the seq directory . . as any jbrowse directory would.  

 

 

Nathan

 

On Apr 8, 2016, at 3:57 AM, matthew couchman (JIC) <[hidden email]> wrote:

 

Hi,

 

I’m installing WebApollo for the first time and I have a question regarding the Configure and Data Generation pages. The pages use /opt/apollo/ as a home for Apollo data but I’m not sure where to set this as the Apollo data directory. I’ve seen some references to a config.properties file but I can’t find that in my v2.0.2 download.

 

Thanks in advance for your help,

 

                                Matt.




This list is for the Apollo Annotation Editing Tool. Info at 
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to 
[hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

 





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apollo-create-organism.jpg (33K) Download Attachment
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Re: Initial configuration

nathandunn

Sometimes it logs out on you silently without letting you know (its a known bug).  If you refresh it should fix this.    When log on, try clicking on the “Remember me” checkbox, which should preserve your session for a year.  Conversely, you can set the session timeout in tomcat for longer than 30 minutes if that helps.  


Nathan

On Apr 8, 2016, at 9:59 AM, matthew couchman (JIC) <[hidden email]> wrote:

Hi Nathan,
 
Thanks for your reply, that’s cleared that up though I have a further problem now: the text boxes are greyed out and show a no entry cursor when I mouse over them. The admin tab says “Problem loading admin page”. Do you know where I need to look to remedy this?
 
Many thanks,
 
                                Matt.
 
 
From: [hidden email] [[hidden email]] On Behalf Of Nathan Dunn
Sent: 08 April 2016 15:26
To: [hidden email]
Subject: Re: [apollo] Initial configuration
 
 
If you are installing 2.0.2 you set data per organism.  For example, if you had two organisms (e.g., cow and dog), you would might put your jbrowse data in a directory /opt/apollo/cow and /research/disk2/dog,  respectively.   
 
When creating the organism you would point to those directories, which would contain trackList.json and the seq directory . . as any jbrowse directory would.  
 
<image001.png>
 
Nathan
 
On Apr 8, 2016, at 3:57 AM, matthew couchman (JIC) <[hidden email]> wrote:
 
Hi,
 
I’m installing WebApollo for the first time and I have a question regarding the Configure and Data Generation pages. The pages use /opt/apollo/ as a home for Apollo data but I’m not sure where to set this as the Apollo data directory. I’ve seen some references to a config.properties file but I can’t find that in my v2.0.2 download.
 
Thanks in advance for your help,
 
                                Matt.



This list is for the Apollo Annotation Editing Tool. Info at 
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to 
[hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
 
<apollo-create-organism.jpg>


This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.