[apollo] New Apollo Release 2.0.3 (JB1.12.2-apollo)

Discussion:

Monica Munoz-Torres

2016-06-16 02:15:01 UTC

*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:
https://github.com/GMOD/Apollo/releases/

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

*** 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:*

- Browse the Troubleshooting guide at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
- Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
- Post your questions on our mailing list at ***@lists.lbl.gov

** 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,
The Apollo Development Team <http://genomearchitect.org/about/>

[image: 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

Ohm, R.A. (Robin)

2016-07-03 14:30:59 UTC

Permalink

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: apollo-***@lists.lbl.gov [apollo-***@lists.lbl.gov] on behalf of Monica Munoz-Torres [***@lbl.gov]
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:
https://github.com/GMOD/Apollo/releases/

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

* 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:

* Browse the Troubleshooting guide at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
* Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
* Post your questions on our mailing list at ***@lists.lbl.gov<mailto:***@lists.lbl.gov>

* 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,
The Apollo Development Team<http://genomearchitect.org/about/>

[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<http://www.AlexanderWild.com> | DNA image from ShutterStock.com<http://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

Nathan Dunn

2016-07-03 14:52:11 UTC

Permalink

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

https://nodejs.org/en/download/ <https://nodejs.org/en/download/>

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 doesnât work, please send more of the original stack trace.

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

Post by Ohm, R.A. (Robin)
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
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
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
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.
https://github.com/GMOD/Apollo/releases/ <https://github.com/GMOD/Apollo/releases/>
http://genomearchitect.readthedocs.io/ <http://genomearchitect.readthedocs.io/en/stable/>
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html <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 <http://genomearchitect.readthedocs.io/en/latest/Migration.html>
Browse the Troubleshooting guide at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
Open a GitHub issue at https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/>
* The Apollo User Guide is available at http://genomearchitect.org/users-guide/ <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/ <http://genomearchitect.org/demo/>
https://github.com/GMOD/Apollo/blob/master/README.md <https://github.com/GMOD/Apollo/blob/master/README.md>
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
<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 <http://www.alexanderwild.com/> | DNA image from ShutterStock.com <http://shutterstock.com/>
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
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/ <http://genomearchitect.org/>

Nathan Dunn

2016-07-06 14:30:05 UTC

Permalink

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 couldnât 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 <https://github.com/GMOD/Apollo/issues/1161>.

Nathan

Post by Nathan Dunn
You have to install node.js (which includes npm) and install bower (which Iâd intended to make automatic, but failed to).
https://nodejs.org/en/download/ <https://nodejs.org/en/download/>
npm install -g bower
(may need sudo depending on how you install node.js)
./apollo clean-all
./apollo deploy
If that doesnât work, please send more of the original stack trace.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory