Copy Jbrowse data into Apollo

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Copy Jbrowse data into Apollo

Sofia Robb
Hello,

I have a Jbrowse instance all set up, can I copy my jbrowse data dir into my apollo directory? Or should I rerun all the bin/prepare-refseqs.pl and bin/flatfile-to-json.pl steps?

Thanks,
Sofia




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Re: [Gmod-ajax] Copy Jbrowse data into Apollo

Sofia Robb
Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048">404-692-2048
[hidden email]






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: [Gmod-ajax] Copy Jbrowse data into Apollo

nathandunn

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" class="">404-692-2048
[hidden email]





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: [Gmod-ajax] Copy Jbrowse data into Apollo

Sofia Robb
Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
[hidden email]





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: [Gmod-ajax] Copy Jbrowse data into Apollo

nathandunn

In theory it will just whatever JBrowse gives it and rewrite some types. 

Hopefully we can fix it if for some reason it does fail.

Nathan

On Nov 5, 2015, at 11:20 AM, Sofia Robb <[hidden email]> wrote:

Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank" class="">404-692-2048
[hidden email]





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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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: [Gmod-ajax] Copy Jbrowse data into Apollo

Sofia Robb
Approximately how long does the process of creating a new organism take? I started mine about an hour ago and my browser still says "Processing ...". Is this normal?

Thanks for all the info!

On Thu, Nov 5, 2015 at 1:08 PM, Nathan Dunn <[hidden email]> wrote:

In theory it will just whatever JBrowse gives it and rewrite some types. 

Hopefully we can fix it if for some reason it does fail.

Nathan

On Nov 5, 2015, at 11:20 AM, Sofia Robb <[hidden email]> wrote:

Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
[hidden email]





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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https://lists.sourceforge.net/lists/listinfo/gmod-ajax








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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: [Gmod-ajax] Copy Jbrowse data into Apollo

Colin
Hi Sofia

I think sometimes the "Processing" step doesn't update you properly, but it should finish pretty quick. You can try a page refresh and see if your genome is loaded, and you don't have to worry about it interrupting anything with your page refresh (the processing step doesn't do anything complicated really, and the server basically has all the info it needs as soon as your click the button).

If you do have a very large number of scaffolds, you can see some delays, but otherwise, it should be fine.


-Colin

On Thu, Nov 5, 2015 at 2:23 PM, Sofia Robb <[hidden email]> wrote:
Approximately how long does the process of creating a new organism take? I started mine about an hour ago and my browser still says "Processing ...". Is this normal?

Thanks for all the info!

On Thu, Nov 5, 2015 at 1:08 PM, Nathan Dunn <[hidden email]> wrote:

In theory it will just whatever JBrowse gives it and rewrite some types. 

Hopefully we can fix it if for some reason it does fail.

Nathan

On Nov 5, 2015, at 11:20 AM, Sofia Robb <[hidden email]> wrote:

Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
[hidden email]





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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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: [Gmod-ajax] Copy Jbrowse data into Apollo

nathandunn

In addition to what Colin said, the amount of memory and your database might also be a factor . . but probably a refresh will suffice to let you know.

Suggested memory settings are below (I’ve done 100K in about 10 minutes). 

On Nov 5, 2015, at 12:30 PM, Colin <[hidden email]> wrote:

Hi Sofia

I think sometimes the "Processing" step doesn't update you properly, but it should finish pretty quick. You can try a page refresh and see if your genome is loaded, and you don't have to worry about it interrupting anything with your page refresh (the processing step doesn't do anything complicated really, and the server basically has all the info it needs as soon as your click the button).

If you do have a very large number of scaffolds, you can see some delays, but otherwise, it should be fine.


-Colin

On Thu, Nov 5, 2015 at 2:23 PM, Sofia Robb <[hidden email]> wrote:
Approximately how long does the process of creating a new organism take? I started mine about an hour ago and my browser still says "Processing ...". Is this normal?

Thanks for all the info!

On Thu, Nov 5, 2015 at 1:08 PM, Nathan Dunn <[hidden email]> wrote:

In theory it will just whatever JBrowse gives it and rewrite some types. 

Hopefully we can fix it if for some reason it does fail.

Nathan

On Nov 5, 2015, at 11:20 AM, Sofia Robb <[hidden email]> wrote:

Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank" class="">404-692-2048
[hidden email]





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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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax








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: [Gmod-ajax] Copy Jbrowse data into Apollo

Sofia Robb
In reply to this post by nathandunn
Ok, yes! I was able to point to my jbrowse data directory and it worked great, includes and all! I had some memory issue, but got those worked out. Turns out that with my system (centOS7) I needed to add my CATALINA_OPT to my tomcat.conf file. Found this out by checking out my tomcat start up script, which wasn't catalina.sh. It was a bit of a goose chase but we got it figured out. Thank you everyone!!

Sofia


On Thu, Nov 5, 2015 at 1:08 PM, Nathan Dunn <[hidden email]> wrote:

In theory it will just whatever JBrowse gives it and rewrite some types. 

Hopefully we can fix it if for some reason it does fail.

Nathan

On Nov 5, 2015, at 11:20 AM, Sofia Robb <[hidden email]> wrote:

Ok. Thanks! Does Apollo 2 handle includes, like in my JBrowse trackList.json?

{
   "tracks" : [
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "include" : [
      "includes/DNA.json",
      "includes/smednr.reduced_genes.json",
      "includes/smednr.filtered_genes.json",
      "includes/smednr.repeat_genes.json",
      "includes/smednr.redundant_genes.json",
      "includes/urbana.reduced_genes.json",
      "includes/urbana.filtered_genes.json",
      "includes/urbana.repeat_genes.json",
      "includes/033226_uniq.reduced_genes.json",
      "includes/unigenes.reduced_genes.json",
   ],
   "dataset_id" : "SmedSxl_v31",
   "formatVersion" : 1
}

On Thu, Nov 5, 2015 at 11:28 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo 2 you should be able to just point that jbrowse directory when creating an organism.   

There should not be any additional configuration over what you did for JBrowse and it doesn’t write to that directory.

Nathan

On Nov 5, 2015, at 9:44 AM, Sofia Robb <[hidden email]> wrote:

Thanks. I am going to try it.

On Thu, Nov 5, 2015 at 10:42 AM, Eric Rasche <[hidden email]> wrote:
Hi Sofia,

I've had success just copying those data folders so far :)

Ciao,
Eric

On 11/05/2015 11:41 AM, Sofia Robb wrote:
> Hello,
>
> I have a Jbrowse instance all set up, can I copy my jbrowse data dir
> into my apollo directory? Or should I rerun all
> the bin/prepare-refseqs.pl <http://prepare-refseqs.pl> and
> bin/flatfile-to-json.pl <http://flatfile-to-json.pl> steps?
>
> Thanks,
> Sofia
>
>
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
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