New Apollo Release 2.0.3 (JB1.12.2-apollo)

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New Apollo Release 2.0.3 (JB1.12.2-apollo)

Monica Munoz-Torres
We are pleased to announce the latest Apollo release
Apollo 2.0.3

Some of the new features include: 
  • Ability to export Apollo annotations into a Chado database - and ability to update an existing Chado database.
  • Users now have the ability to change the type of genomic element they are annotating after it has been dragged to the User-created Annotations area (e.g. from 'gene' to 'pseudogene')
  • Users can now have multiple tabs open while simultaneously annotating genomic elements for 2 or more different organisms.
  • Usernames are no longer restricted to email addresses.
  • We have upgraded the JBrowse version to 1.12.2-apollo

Some important fixes include: 
  • Users can now annotate genomic elements using evidence from Canvas tracks, using the 'right-click' menu options. 
  • Comments are no longer restricted to only 256 characters. 
  • The error caused from 'Undo' operations on a pseudogene has been fixed.

* The latest release can be downloaded from GitHub at:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 
http://genomearchitect.readthedocs.io/

* A more detailed account of all changes is available in the Apollo ChangeLog: 
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: 
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

* Migrating existing annotations: You will need to migrate existing annotations from Web Apollo 1.0.x. Please find detailed information about migrating annotations at http://genomearchitect.readthedocs.io/en/latest/Migration.html

* Troubleshooting, GitHub tracker, Mailing List: 

* The Apollo User Guide is available at http://genomearchitect.org/users-guide/

* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/

These and more details are available from the README file on the Apollo repository: 
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to your questions and suggestions. 

Sincerely, 


Inline image 1
It is very likely you will receive this message more than once. We offer our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from ShutterStock.com

--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




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: New Apollo Release 2.0.3 (JB1.12.2-apollo)

Robin A. Ohm
Hi Monica,

I'm trying to upgrade from version 2.0.2 to 2.0.3, but I've run into a problem. After I copy the war file to the tomcat webapps dir and start tomcat, the genome browser shows the login page. I log in, but then it freezes, with just a message "Loading...".

During "./apollo deploy" I got several warning messages (I pasted some of the output below), which I don't remember seeing before. I'm not sure what they mean, but could they be related somehow?

I've rolled back to version 2.0.2 for now, and that still works fine. Any help would be greatly appreciated! 

Best regards,

Robin

 [...]

BUILD SUCCESSFUL

Total time: 1 mins 45.858 secs

| Compiling 15 source files

| Compiling 209 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 306 source files

| Warning The [$tt__setCurrentOrganism] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__setCurrentSequence] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__index] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__show] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__save] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null

[...]



Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Monica Munoz-Torres [[hidden email]]
Sent: Thursday, June 16, 2016 4:15
To: Apollo List
Subject: [apollo] New Apollo Release 2.0.3 (JB1.12.2-apollo)

We are pleased to announce the latest Apollo release
Apollo 2.0.3

Some of the new features include: 
  • Ability to export Apollo annotations into a Chado database - and ability to update an existing Chado database.
  • Users now have the ability to change the type of genomic element they are annotating after it has been dragged to the User-created Annotations area (e.g. from 'gene' to 'pseudogene')
  • Users can now have multiple tabs open while simultaneously annotating genomic elements for 2 or more different organisms.
  • Usernames are no longer restricted to email addresses.
  • We have upgraded the JBrowse version to 1.12.2-apollo

Some important fixes include: 
  • Users can now annotate genomic elements using evidence from Canvas tracks, using the 'right-click' menu options. 
  • Comments are no longer restricted to only 256 characters. 
  • The error caused from 'Undo' operations on a pseudogene has been fixed.

* The latest release can be downloaded from GitHub at:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 
http://genomearchitect.readthedocs.io/

* A more detailed account of all changes is available in the Apollo ChangeLog: 
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: 
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

* Migrating existing annotations: You will need to migrate existing annotations from Web Apollo 1.0.x. Please find detailed information about migrating annotations at http://genomearchitect.readthedocs.io/en/latest/Migration.html

* Troubleshooting, GitHub tracker, Mailing List: 

* The Apollo User Guide is available at http://genomearchitect.org/users-guide/

* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/

These and more details are available from the README file on the Apollo repository: 
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to your questions and suggestions. 

Sincerely, 


Inline image 1
It is very likely you will receive this message more than once. We offer our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from ShutterStock.com

--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




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: New Apollo Release 2.0.3 (JB1.12.2-apollo)

nathandunn

You have to install node.js (which includes npm) and install bower (which I’d intended to make automatic, but failed to).  


To install bower:

npm install -g bower 

(may need sudo depending on how you install node.js) 

Then:

./apollo clean-all
./apollo deploy 

If that doesn’t work, please send more of the original stack trace. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Jul 3, 2016, at 7:30 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Monica,

I'm trying to upgrade from version 2.0.2 to 2.0.3, but I've run into a problem. After I copy the war file to the tomcat webapps dir and start tomcat, the genome browser shows the login page. I log in, but then it freezes, with just a message "Loading...".

During "./apollo deploy" I got several warning messages (I pasted some of the output below), which I don't remember seeing before. I'm not sure what they mean, but could they be related somehow?

I've rolled back to version 2.0.2 for now, and that still works fine. Any help would be greatly appreciated! 

Best regards,

Robin

 [...]

BUILD SUCCESSFUL

Total time: 1 mins 45.858 secs

| Compiling 15 source files

| Compiling 209 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 306 source files

| Warning The [$tt__setCurrentOrganism] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__setCurrentSequence] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__index] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__show] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__save] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null

[...]



Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Monica Munoz-Torres [[hidden email]]
Sent: Thursday, June 16, 2016 4:15
To: Apollo List
Subject: [apollo] New Apollo Release 2.0.3 (JB1.12.2-apollo)

We are pleased to announce the latest Apollo release
Apollo 2.0.3

Some of the new features include: 
  • Ability to export Apollo annotations into a Chado database - and ability to update an existing Chado database.
  • Users now have the ability to change the type of genomic element they are annotating after it has been dragged to the User-created Annotations area (e.g. from 'gene' to 'pseudogene')
  • Users can now have multiple tabs open while simultaneously annotating genomic elements for 2 or more different organisms.
  • Usernames are no longer restricted to email addresses.
  • We have upgraded the JBrowse version to 1.12.2-apollo

Some important fixes include: 
  • Users can now annotate genomic elements using evidence from Canvas tracks, using the 'right-click' menu options. 
  • Comments are no longer restricted to only 256 characters. 
  • The error caused from 'Undo' operations on a pseudogene has been fixed.

* The latest release can be downloaded from GitHub at:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 
http://genomearchitect.readthedocs.io/

* A more detailed account of all changes is available in the Apollo ChangeLog: 
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: 
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

* Migrating existing annotations: You will need to migrate existing annotations from Web Apollo 1.0.x. Please find detailed information about migrating annotations at http://genomearchitect.readthedocs.io/en/latest/Migration.html

* Troubleshooting, GitHub tracker, Mailing List: 

* The Apollo User Guide is available at http://genomearchitect.org/users-guide/

* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/

These and more details are available from the README file on the Apollo repository: 
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to your questions and suggestions. 

Sincerely, 


<Hackathon-logo-image.png>
It is very likely you will receive this message more than once. We offer our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from ShutterStock.com

-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720



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: New Apollo Release 2.0.3 (JB1.12.2-apollo)

nathandunn

Looks like the solution was to delete the contents of the Preference table (delete from Preference) and then do the upgrade as there were improperly formatted dates that MySQL was not handling properly.  

I couldn’t reproduce it on my own, but possibly there was an error introduced by an insertion script.   More details in https://github.com/GMOD/Apollo/issues/1161.  

Nathan

On Jul 3, 2016, at 7:52 AM, Nathan Dunn <[hidden email]> wrote:


You have to install node.js (which includes npm) and install bower (which I’d intended to make automatic, but failed to).  


To install bower:

npm install -g bower 

(may need sudo depending on how you install node.js) 

Then:

./apollo clean-all
./apollo deploy 

If that doesn’t work, please send more of the original stack trace. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Jul 3, 2016, at 7:30 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Monica,

I'm trying to upgrade from version 2.0.2 to 2.0.3, but I've run into a problem. After I copy the war file to the tomcat webapps dir and start tomcat, the genome browser shows the login page. I log in, but then it freezes, with just a message "Loading...".

During "./apollo deploy" I got several warning messages (I pasted some of the output below), which I don't remember seeing before. I'm not sure what they mean, but could they be related somehow?

I've rolled back to version 2.0.2 for now, and that still works fine. Any help would be greatly appreciated! 

Best regards,

Robin

 [...]

BUILD SUCCESSFUL

Total time: 1 mins 45.858 secs

| Compiling 15 source files

| Compiling 209 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 306 source files

| Warning The [$tt__setCurrentOrganism] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__setCurrentSequence] action in [org.bbop.apollo.AnnotatorController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__index] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__show] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null
| Warning The [$tt__save] action in [org.bbop.apollo.AvailableStatusController] accepts a parameter of type [org.springframework.transaction.TransactionStatus].  Interface types and abstract class types are not supported as command objects.  This parameter will be ignored.

null

[...]



Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Monica Munoz-Torres [[hidden email]]
Sent: Thursday, June 16, 2016 4:15
To: Apollo List
Subject: [apollo] New Apollo Release 2.0.3 (JB1.12.2-apollo)

We are pleased to announce the latest Apollo release
Apollo 2.0.3

Some of the new features include: 
  • Ability to export Apollo annotations into a Chado database - and ability to update an existing Chado database.
  • Users now have the ability to change the type of genomic element they are annotating after it has been dragged to the User-created Annotations area (e.g. from 'gene' to 'pseudogene')
  • Users can now have multiple tabs open while simultaneously annotating genomic elements for 2 or more different organisms.
  • Usernames are no longer restricted to email addresses.
  • We have upgraded the JBrowse version to 1.12.2-apollo

Some important fixes include: 
  • Users can now annotate genomic elements using evidence from Canvas tracks, using the 'right-click' menu options. 
  • Comments are no longer restricted to only 256 characters. 
  • The error caused from 'Undo' operations on a pseudogene has been fixed.

* The latest release can be downloaded from GitHub at:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 
http://genomearchitect.readthedocs.io/

* A more detailed account of all changes is available in the Apollo ChangeLog: 
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: 
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

* Migrating existing annotations: You will need to migrate existing annotations from Web Apollo 1.0.x. Please find detailed information about migrating annotations at http://genomearchitect.readthedocs.io/en/latest/Migration.html

* Troubleshooting, GitHub tracker, Mailing List: 

* The Apollo User Guide is available at http://genomearchitect.org/users-guide/

* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/

These and more details are available from the README file on the Apollo repository: 
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to your questions and suggestions. 

Sincerely, 


<Hackathon-logo-image.png>
It is very likely you will receive this message more than once. We offer our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from ShutterStock.com

-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720



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.