[apollo] 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.

[Nathan Dunn]

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

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/ <http://genomearchitect.org/>

[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: apollo-***@lists.lbl.gov [mailto:apollo-***@lists.lbl.gov] On Behalf Of Nathan Dunn
Sent: 08 April 2016 15:26
To: ***@lists.lbl.gov
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.

[cid:***@01D191BE.EABA59B0]

Nathan

On Apr 8, 2016, at 3:57 AM, matthew couchman (JIC) <***@jic.ac.uk<mailto:***@jic.ac.uk>> 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/
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[Nathan Dunn]

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

Post by 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.
Sent: 08 April 2016 15:26
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
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/ <http://genomearchitect.org/>
<apollo-create-organism.jpg>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>