problems creating an organism in apollo

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problems creating an organism in apollo

Willett, Christopher S
Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

 p.s. here is the JSON file if that tells you anything:

{
   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "chunkSize" : 20000,
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "type" : "SequenceTrack",
         "category" : "Reference sequence",
         "seqType" : "dna",
         "key" : "Reference sequence"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "Maker_fulld_Gff",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
         "compress" : 0,
         "type" : "FeatureTrack",
         "label" : "Maker_fulld_Gff"
      }
   ],
   "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625






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: problems creating an organism in apollo

nathandunn

You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

> On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:
>
> Hello-
>
> I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).
>
> One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:
>
> Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
>
> Any help you could provide would be appreciated,
>
> Thanks,
>
> Best,
>
> Chris Willett
>
>  p.s. here is the JSON file if that tells you anything:
>
> {
>    "tracks" : [
>       {
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "chunkSize" : 20000,
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
>          "label" : "DNA",
>          "type" : "SequenceTrack",
>          "category" : "Reference sequence",
>          "seqType" : "dna",
>          "key" : "Reference sequence"
>       },
>       {
>          "style" : {
>             "className" : "feature"
>          },
>          "key" : "Maker_fulld_Gff",
>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>          "trackType" : null,
>          "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
>          "compress" : 0,
>          "type" : "FeatureTrack",
>          "label" : "Maker_fulld_Gff"
>       }
>    ],
>    "formatVersion" : 1
> }
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280
>
> Office: 2252 Genome Science Building
> phone:
> 919-843-8663
> fax:
> 919-962-1625
>
> http://labs.bio.unc.edu/Willett/
>
>
>
>
> 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: problems creating an organism in apollo

Willett, Christopher S
Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625






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: problems creating an organism in apollo

nathandunn

So, I just tested this (looks like you are probably using the latest pre-release), and just worked for me (./apollo run-local 8082 . .. connect on http://localhost:8082/apollo and added the volvox organism from jbrowse). 

If you are running the server locally, those data files should be visible locally, so you can either copy them there, or create an organism that points to the visible directory.  

Nathan

On Jul 25, 2016, at 2:05 PM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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.

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Re: problems creating an organism in apollo

nathandunn

I realized that I am also getting this error when I use docker and pre-register a user using the ```apollo-config.groovy``` file:


I will fix that shortly.  If are NOT explicitly register an admin user, using the apollo-config.groovy file and are still getting this error, please let me know what steps you are taking (though they seemed pretty straight-forward) and I’ll see what I can do. 

I should have this fixed within the day. 

Nathan

On Jul 25, 2016, at 3:15 PM, Nathan Dunn <[hidden email]> wrote:


So, I just tested this (looks like you are probably using the latest pre-release), and just worked for me (./apollo run-local 8082 . .. connect on http://localhost:8082/apollo and added the volvox organism from jbrowse). 

If you are running the server locally, those data files should be visible locally, so you can either copy them there, or create an organism that points to the visible directory.  

Nathan

On Jul 25, 2016, at 2:05 PM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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: problems creating an organism in apollo

Willett, Christopher S
Hi Nathan-

I tried connecting with the other port (8082) as you suggest below but I wasn’t sure what you were suggesting I do after I open the browser window. Are you saying that I should add volvox from jbrowse to test it or that it would be there already (I don’t see it in the pull down menu). I am still seeing the same types of errors I listed below when I setup and login this way as well (log from terminal pasted in below).

I wasn’t  attempting to use the apollo-config.groovy file to log-in. I am just launching apollo locally from within the Apollo-2.0.4-RC1 directory and then going to it on chrome (I tried safari as well). Yesterday I tried to setup and launch the 2.0.3 version (I hadn’t realized 2.0.4 was pre-release initially) but I was having trouble getting it running (perhaps due to conflicts with dependences I had set up for the 2.0.4 version?)  

Thanks again for your help,

Chris



biology731:~ cwillett$ cd /Applications/ngs_apps/Apollo-2.0.4-RC1
biology731:Apollo-2.0.4-RC1 cwillett$ ./apollo run-local 8082
Gradle not found using gradlew
Defining custom 'build' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0
No log file found in classpath.
final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Copying apollo plugin
handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:copyApolloPlugin UP-TO-DATE
:installJBrowsePlugins
installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse-download/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.
:handleJBrowse
:copy.apollo.plugin.webapp
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 20.334 secs

| Compiling 3 source files
..lopmentGrails 2.5.5rguide/gradle_daemon.html
| Compiling 3 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
objc[36158]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
Configuring Shiro ...
Shiro Configured

| Server running. Browse to http://localhost:8082/apollo
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:16,398 [http-bio-8082-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-26 09:52:16,405 [http-bio-8082-exec-5] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-26 09:52:16,405 [http-bio-8082-exec-5] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-2] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-10] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-2] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-10] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:44,459 [http-bio-8082-exec-8] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-26 09:52:44,463 [http-bio-8082-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-26 09:52:44,694 [http-bio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-07-26 09:53:12,395 [http-bio-8082-exec-6] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.
 
On Jul 26, 2016, at 12:30 AM, Nathan Dunn <[hidden email]> wrote:


I realized that I am also getting this error when I use docker and pre-register a user using the ```apollo-config.groovy``` file:


I will fix that shortly.  If are NOT explicitly register an admin user, using the apollo-config.groovy file and are still getting this error, please let me know what steps you are taking (though they seemed pretty straight-forward) and I’ll see what I can do. 

I should have this fixed within the day. 

Nathan

On Jul 25, 2016, at 3:15 PM, Nathan Dunn <[hidden email]> wrote:


So, I just tested this (looks like you are probably using the latest pre-release), and just worked for me (./apollo run-local 8082 . .. connect on http://localhost:8082/apollo and added the volvox organism from jbrowse). 

If you are running the server locally, those data files should be visible locally, so you can either copy them there, or create an organism that points to the visible directory.  

Nathan

On Jul 25, 2016, at 2:05 PM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625






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: problems creating an organism in apollo

nathandunn

I tested this with the RC1 version and it worked fine.  The errors that you are getting below should be okay, it just indicates that you need to add an organism.  What happens if you follow the direction here?


You can use this yeast data:



You should point it to (an absolute directory) wherever you decompress it. 

The data has to be there before you add the organism as it has to build the scaffold internally (you can always add additional tracks and update configs later, though). 

Nathan

On Jul 26, 2016, at 7:17 AM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

I tried connecting with the other port (8082) as you suggest below but I wasn’t sure what you were suggesting I do after I open the browser window. Are you saying that I should add volvox from jbrowse to test it or that it would be there already (I don’t see it in the pull down menu). I am still seeing the same types of errors I listed below when I setup and login this way as well (log from terminal pasted in below).

I wasn’t  attempting to use the apollo-config.groovy file to log-in. I am just launching apollo locally from within the Apollo-2.0.4-RC1 directory and then going to it on chrome (I tried safari as well). Yesterday I tried to setup and launch the 2.0.3 version (I hadn’t realized 2.0.4 was pre-release initially) but I was having trouble getting it running (perhaps due to conflicts with dependences I had set up for the 2.0.4 version?)  

Thanks again for your help,

Chris



biology731:~ cwillett$ cd /Applications/ngs_apps/Apollo-2.0.4-RC1
biology731:Apollo-2.0.4-RC1 cwillett$ ./apollo run-local 8082
Gradle not found using gradlew
Defining custom 'build' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0
No log file found in classpath.
final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Copying apollo plugin
handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:copyApolloPlugin UP-TO-DATE
:installJBrowsePlugins
installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse-download/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.
:handleJBrowse
:copy.apollo.plugin.webapp
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 20.334 secs

| Compiling 3 source files
..lopmentGrails 2.5.5rguide/gradle_daemon.html
| Compiling 3 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
objc[36158]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
Configuring Shiro ...
Shiro Configured

| Server running. Browse to http://localhost:8082/apollo
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:16,398 [http-bio-8082-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-26 09:52:16,405 [http-bio-8082-exec-5] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-26 09:52:16,405 [http-bio-8082-exec-5] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-2] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-10] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-2] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-10] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:44,459 [http-bio-8082-exec-8] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-26 09:52:44,463 [http-bio-8082-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-26 09:52:44,694 [http-bio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-07-26 09:53:12,395 [http-bio-8082-exec-6] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.
 
On Jul 26, 2016, at 12:30 AM, Nathan Dunn <[hidden email]> wrote:


I realized that I am also getting this error when I use docker and pre-register a user using the ```apollo-config.groovy``` file:


I will fix that shortly.  If are NOT explicitly register an admin user, using the apollo-config.groovy file and are still getting this error, please let me know what steps you are taking (though they seemed pretty straight-forward) and I’ll see what I can do. 

I should have this fixed within the day. 

Nathan

On Jul 25, 2016, at 3:15 PM, Nathan Dunn <[hidden email]> wrote:


So, I just tested this (looks like you are probably using the latest pre-release), and just worked for me (./apollo run-local 8082 . .. connect on http://localhost:8082/apollo and added the volvox organism from jbrowse). 

If you are running the server locally, those data files should be visible locally, so you can either copy them there, or create an organism that points to the visible directory.  

Nathan

On Jul 25, 2016, at 2:05 PM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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Re: problems creating an organism in apollo

nathandunn

Resolved.  It looked like it was a path problem. 

Nathan

On Jul 26, 2016, at 9:28 AM, Nathan Dunn <[hidden email]> wrote:


I tested this with the RC1 version and it worked fine.  The errors that you are getting below should be okay, it just indicates that you need to add an organism.  What happens if you follow the direction here?


You can use this yeast data:

<yeast.tgz>

You should point it to (an absolute directory) wherever you decompress it. 

The data has to be there before you add the organism as it has to build the scaffold internally (you can always add additional tracks and update configs later, though). 

Nathan

On Jul 26, 2016, at 7:17 AM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

I tried connecting with the other port (8082) as you suggest below but I wasn’t sure what you were suggesting I do after I open the browser window. Are you saying that I should add volvox from jbrowse to test it or that it would be there already (I don’t see it in the pull down menu). I am still seeing the same types of errors I listed below when I setup and login this way as well (log from terminal pasted in below).

I wasn’t  attempting to use the apollo-config.groovy file to log-in. I am just launching apollo locally from within the Apollo-2.0.4-RC1 directory and then going to it on chrome (I tried safari as well). Yesterday I tried to setup and launch the 2.0.3 version (I hadn’t realized 2.0.4 was pre-release initially) but I was having trouble getting it running (perhaps due to conflicts with dependences I had set up for the 2.0.4 version?)  

Thanks again for your help,

Chris



biology731:~ cwillett$ cd /Applications/ngs_apps/Apollo-2.0.4-RC1
biology731:Apollo-2.0.4-RC1 cwillett$ ./apollo run-local 8082
Gradle not found using gradlew
Defining custom 'build' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0
No log file found in classpath.
final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Copying apollo plugin
handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
:copyApolloPlugin UP-TO-DATE
:installJBrowsePlugins
installing jbrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse-download/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid.
:handleJBrowse
:copy.apollo.plugin.webapp
[ant:echo] Copying WebApollo plugin to jbrowse webapp ...
:setup-jbrowse
:copy-resources
:copyResourcesDev
found jbrowse directory false
Installing Perl prerequisites ...Prerequisites installed, finished.
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 1 mins 20.334 secs

| Compiling 3 source files
..lopmentGrails 2.5.5rguide/gradle_daemon.html
| Compiling 3 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
objc[36158]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
Configuring Shiro ...
Shiro Configured

| Server running. Browse to http://localhost:8082/apollo
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:16,398 [http-bio-8082-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-26 09:52:16,405 [http-bio-8082-exec-5] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-26 09:52:16,405 [http-bio-8082-exec-5] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-2] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,482 [http-bio-8082-exec-10] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-2] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-26 09:52:16,511 [http-bio-8082-exec-10] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-26 09:52:44,459 [http-bio-8082-exec-8] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-26 09:52:44,463 [http-bio-8082-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-26 09:52:44,694 [http-bio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-07-26 09:53:12,395 [http-bio-8082-exec-6] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.
 
On Jul 26, 2016, at 12:30 AM, Nathan Dunn <[hidden email]> wrote:


I realized that I am also getting this error when I use docker and pre-register a user using the ```apollo-config.groovy``` file:


I will fix that shortly.  If are NOT explicitly register an admin user, using the apollo-config.groovy file and are still getting this error, please let me know what steps you are taking (though they seemed pretty straight-forward) and I’ll see what I can do. 

I should have this fixed within the day. 

Nathan

On Jul 25, 2016, at 3:15 PM, Nathan Dunn <[hidden email]> wrote:


So, I just tested this (looks like you are probably using the latest pre-release), and just worked for me (./apollo run-local 8082 . .. connect on http://localhost:8082/apollo and added the volvox organism from jbrowse). 

If you are running the server locally, those data files should be visible locally, so you can either copy them there, or create an organism that points to the visible directory.  

Nathan

On Jul 25, 2016, at 2:05 PM, Willett, Christopher S <[hidden email]> wrote:

Hi Nathan-

Thanks for getting back to me. If I log off and log-in, I still can’t add an organism and the following set of errors come up in the terminal:

| Error 2016-07-25 16:36:09,807 [http-bio-8080-exec-6] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:09,808 [http-bio-8080-exec-9] ERROR apollo.PermissionService  - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-6] ERROR apollo.GroupController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
| Error 2016-07-25 16:36:09,810 [http-bio-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService  - Not implemented without a token
2016-07-25 16:36:09,811 [http-bio-8080-exec-1] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-1] ERROR apollo.UserController  - Failed to authenticate
| Error 2016-07-25 16:36:09,811 [http-bio-8080-exec-9] ERROR apollo.UserController  - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
| Error 2016-07-25 16:36:15,927 [http-bio-8080-exec-5] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
| Error 2016-07-25 16:36:15,939 [http-bio-8080-exec-7] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2016-07-25 16:36:16,153 [http-bio-8080-exec-7] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

I wasn’t sure where the program would look for the data files. They are at the base directory of the hard drive that has the applications including the apollo directory on my computer (e.g. the datafilee are at /Volumes/TopherPro/opt/apollo/data/). That opt/apollo/data directory has the files you list (without the names file). On this mac my home directory is on a separate hard drive (/Volumes/willett_twins/cwillett/). Should I move these directories there? 

Thanks again,

Chris


On Jul 25, 2016, at 4:15 PM, Nathan Dunn <[hidden email]> wrote:


You are probably running out of master, but it should still work.

If you log out (upper-right) and log back in does it allow you to add the organism?  If not, what do you see on the terminal?

The directory path you should use would be like (if you are using home as a directory):

/Users/nathandunn/mygenomicdata/T_californicus/

if you did a list like this:

ls /Users/nathandunn/mygenomicdata/T_californicus/

should give you something like this:

names seq tracks
trackList.json tracks.conf



Nathan

On Jul 25, 2016, at 1:04 PM, Willett, Christopher S <[hidden email]> wrote:

Hello-

I am trying to run Apollo locally to look at a new annotation that I have done of a non-model species using Maker. I am having some issues getting Apollo to find the data that I have added to Apollo. I hope I am not missing anything obvious but I think I followed all the steps in your quick-start guide. I am running Apollo 2.0.4 via terminal on a Mac. The Apollo browser loads when I access it at the default web address but then when I try to create an organism I get the error “Organism directory must be an absolute path pointing to ‘trackList.json’” I had imported the sequence and gff files into opt/apollo as outlined.  I couldn’t find anything other than the suggestion to validate the .json file (I pasted the text from the trackList.json file into JSONLint which said it was a valid json ).

One other potential thing that could be relevant-I get the messages on terminal like this when I first open initiate the Apollo application:

Error 2016-07-25 13:42:21,766 [http-bio-8080-exec-9] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.

Any help you could provide would be appreciated,

Thanks,

Best,

Chris Willett

p.s. here is the JSON file if that tells you anything:

{
  "tracks" : [
     {
        "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
        "chunkSize" : 20000,
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "label" : "DNA",
        "type" : "SequenceTrack",
        "category" : "Reference sequence",
        "seqType" : "dna",
        "key" : "Reference sequence"
     },
     {
        "style" : {
           "className" : "feature"
        },
        "key" : "Maker_fulld_Gff",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "trackType" : null,
        "urlTemplate" : "tracks/Maker_fulld_Gff/{refseq}/trackData.json",
        "compress" : 0,
        "type" : "FeatureTrack",
        "label" : "Maker_fulld_Gff"
     }
  ],
  "formatVersion" : 1
}

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone:
919-843-8663
fax:
919-962-1625

http://labs.bio.unc.edu/Willett/




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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280 

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625





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