[apollo] Issues with Jbrowse in WebApollo 2.0.1 and 2.0.2

[Nathan Henry]

Hi,

I have some issues with 2.0.1 and 2.0.2.

I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The
annotator would work for one browse but subsequent attempts to log in would
not work. The catalina output had a lot of data about broken pipes.

I have tried to isntall 2.0.1 from scratch.

The WebApollo part of the app works. I can log into WebApollo and I can see
the left menu pain but the the Jbrowse pane is white. I can even see the
reference sequence in the WebApollo menu tab "Ref Sequence" after I load a
sequence but there are no tracks listed in the "Tracks" tab. When I try to
use the public link to view plain jbrowse, there is nothing but a white
screen.

My console error is as follows:

ReferenceError: require is not defined

require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],



The catalina logs says:

2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
apollo.PermissionService - Problem authenticating:
org.apache.shiro.authc.AccountException: Null usernames are not allowed by
this realm.

I have also tried to use 2.0.2 with similar results - blank white screen
where jbrowse panel should be while the WebApollo panels work.

Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to
download. The directory "jbrowse-download" has the plugins directory but no
other jbrowse directory. I have downloaded Jbrowse and manually copied the
contents of the Jbrowse file into the "jbrowse-download" directory but I
still get a white screen in the jbrowse pane of webapollo. I have tried
this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6,
and 1.12.1.

I eventually reverted back to 2.0.0 but I believe I am running into the
problem detailed here:
https://github.com/GMOD/Apollo/issues/555

I am using postgres 9.3 as my database.

Does anyone have any suggestions?

Thanks for your time,

Henry

[Nathan Dunn]

Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases <https://github.com/GMOD/Apollo/releases>)? If its the former you’ll want to do a “./apollo clean-all” before you rebuild.

In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory. e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory. You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.

Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
<>
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.
https://github.com/GMOD/Apollo/issues/555 <https://github.com/GMOD/Apollo/issues/555>
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Henry]

Hi Nathan,

I am downloading the tar.gz from the releases page.

Before I deploy to tomcat I delete the war file I am replacing as well as
the directory that tomcat creates when it deploys a new war file. I also
delete the directory under tomcat/work/Catalina/localhost (although I don't
know if this is necessary). I did have older versions of WebApollo in
tomcat so I removed them also. I get the same errors listed above. I am
using version 2.0.1 at this time because Jbrowse seems to download when
running the deploy script for this version.

Do you have other suggestions?

Thank you for your time,

Henry

Post by Nathan Dunn
Also, are you upgrading directly from git or are you uses the downloads on
the source page (https://github.com/GMOD/Apollo/releases)? If its the
former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything
related to apollo from your tomcat webapps directory. e.g., typically the
apollo.war file will explode its contents into a directory called “apollo”
in the webapps directory. You should remove that directory when you
upgrade as you might have stale javascript and other files in there that
might cause problems.
Nathan
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The
annotator would work for one browse but subsequent attempts to log in would
not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can
see the left menu pain but the the Jbrowse pane is white. I can even see
the reference sequence in the WebApollo menu tab "Ref Sequence" after I
load a sequence but there are no tracks listed in the "Tracks" tab. When I
try to use the public link to view plain jbrowse, there is nothing but a
white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are not allowed by
this realm.
I have also tried to use 2.0.2 with similar results - blank white screen
where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to
download. The directory "jbrowse-download" has the plugins directory but no
other jbrowse directory. I have downloaded Jbrowse and manually copied the
contents of the Jbrowse file into the "jbrowse-download" directory but I
still get a white screen in the jbrowse pane of webapollo. I have tried
this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6,
and 1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running into the
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
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2. In the subject line of your email type: unsubscribe apollo | 3. Leave
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[Nathan Dunn]

When it installs JBrowse in 2.0.2 it does a recursive clone of jbrowse to install it (this will be fixed in 2.0.3), which sometimes stalls.

I would suggest doing an “./apollo clean-all” and then an “./apollo deploy”, but tracking the build output in case it fails again you can send out the build information.

If that doesn’t work, we can meet briefly and sort it out.

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

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases <https://github.com/GMOD/Apollo/releases>)? If its the former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory. e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory. You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
<>
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.
https://github.com/GMOD/Apollo/issues/555 <https://github.com/GMOD/Apollo/issues/555>
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Loraine Guéguen]

Hi Henry,

Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu
pain but the Jbrowse pane is white
And error in the catalina logs :
"org.apache.shiro.authc.AccountException: Null usernames are not allowed
by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with
the deploy script, contrary to version 2.0.2), with a postgres database.

Thank you in advance,

Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well
as the directory that tomcat creates when it deploys a new war file. I
also delete the directory under tomcat/work/Catalina/localhost
(although I don't know if this is necessary). I did have older
versions of WebApollo in tomcat so I removed them also. I get the same
errors listed above. I am using version 2.0.1 at this time because
Jbrowse seems to download when running the deploy script for this
version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the
downloads on the source page
(https://github.com/GMOD/Apollo/releases)? If its the former
you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove
everything related to apollo from your tomcat webapps directory.
e.g., typically the apollo.war file will explode its contents into
a directory called “apollo” in the webapps directory. You should
remove that directory when you upgrade as you might have stale
javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some
problems. The annotator would work for one browse but subsequent
attempts to log in would not work. The catalina output had a lot
of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and
I can see the left menu pain but the the Jbrowse pane is white. I
can even see the reference sequence in the WebApollo menu tab
"Ref Sequence" after I load a sequence but there are no tracks
listed in the "Tracks" tab. When I try to use the public link to
view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are not
allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white
screen where jbrowse panel should be while the WebApollo panels
work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem
to download. The directory "jbrowse-download" has the plugins
directory but no other jbrowse directory. I have downloaded
Jbrowse and manually copied the contents of the Jbrowse file into
the "jbrowse-download" directory but I still get a white screen
in the jbrowse pane of webapollo. I have tried this with the
following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and
1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
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
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
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/

--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Loraine Guéguen]

Hi again,

I have just seen that some repositories in jbrowse-download/src/ are
empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?

Thanks

Loraine Guéguen

Post by Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu
pain but the Jbrowse pane is white
"org.apache.shiro.authc.AccountException: Null usernames are not
allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with
the deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as
well as the directory that tomcat creates when it deploys a new war
file. I also delete the directory under
tomcat/work/Catalina/localhost (although I don't know if this is
necessary). I did have older versions of WebApollo in tomcat so I
removed them also. I get the same errors listed above. I am using
version 2.0.1 at this time because Jbrowse seems to download when
running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the
downloads on the source page
(https://github.com/GMOD/Apollo/releases)? If its the former
you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove
everything related to apollo from your tomcat webapps directory.
e.g., typically the apollo.war file will explode its contents
into a directory called “apollo” in the webapps directory. You
should remove that directory when you upgrade as you might have
stale javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some
problems. The annotator would work for one browse but subsequent
attempts to log in would not work. The catalina output had a lot
of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo
and I can see the left menu pain but the the Jbrowse pane is
white. I can even see the reference sequence in the WebApollo
menu tab "Ref Sequence" after I load a sequence but there are no
tracks listed in the "Tracks" tab. When I try to use the public
link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are not
allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank
white screen where jbrowse panel should be while the WebApollo
panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem
to download. The directory "jbrowse-download" has the plugins
directory but no other jbrowse directory. I have downloaded
Jbrowse and manually copied the contents of the Jbrowse file
into the "jbrowse-download" directory but I still get a white
screen in the jbrowse pane of webapollo. I have tried this with
the following versions of Jbrowse with no luck: 1.11.5, 1.11.6,
and 1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
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
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
subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
This list is for the Apollo Annotation Editing Tool. Info athttp://genomearchitect.org/

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Nathan Dunn]

JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse. Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3). I would recommend the 2.0.2 version.

To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”). Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way. After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).

I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).

Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on.

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

Post by Loraine Guéguen
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen

Post by Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the downloads on the source page ( <https://github.com/GMOD/Apollo/releases>https://github.com/GMOD/Apollo/releases <https://github.com/GMOD/Apollo/releases>)? If its the former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory. e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory. You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
<>
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.
https://github.com/GMOD/Apollo/issues/555 <https://github.com/GMOD/Apollo/issues/555>
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Henry]

Hi Loraine,

./apollo clean-all and then ./apollo deploy did not work for me.

Unfortunately, I have not had time to troubleshoot this further.

However, I am sure Nathan and the Apollo team will be able to help sort
this out.

Henry

Post by Nathan Dunn
JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse. Sometimes
github get stuck and the process needs to start over (this is vastly
improved in the master branch, which will become 2.0.3). I would
recommend the 2.0.2 version.
To “unstick it” you have to clean JBrowse as well, which is what clean-all
does (“./apollo clean-all ; ./apollo deploy”). Conversely you can do a
“rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but
clean-all is a better way. After you type “./apollo deploy” please verify
that your jbrowse-download/src is there with multiple directories fully
populated (you should see a “main.js” in the directories).
I think that will fix both problems (the null usernames might just
indicate that you have not registered a user or logged in).
Please post the full logs (clean and build) if anything goes wrong so I
can determine if there is anything else going on.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are empty
after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu
pain but the Jbrowse pane is white
Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the
deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as
the directory that tomcat creates when it deploys a new war file. I also
delete the directory under tomcat/work/Catalina/localhost (although I don't
know if this is necessary). I did have older versions of WebApollo in
tomcat so I removed them also. I get the same errors listed above. I am
using version 2.0.1 at this time because Jbrowse seems to download when
running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry

Post by Nathan Dunn
Also, are you upgrading directly from git or are you uses the downloads
on the source page ( <https://github.com/GMOD/Apollo/releases>
https://github.com/GMOD/Apollo/releases)? If its the former you’ll want
to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything
related to apollo from your tomcat webapps directory. e.g., typically the
apollo.war file will explode its contents into a directory called “apollo”
in the webapps directory. You should remove that directory when you
upgrade as you might have stale javascript and other files in there that
might cause problems.
Nathan
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems.
The annotator would work for one browse but subsequent attempts to log in
would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can
see the left menu pain but the the Jbrowse pane is white. I can even see
the reference sequence in the WebApollo menu tab "Ref Sequence" after I
load a sequence but there are no tracks listed in the "Tracks" tab. When I
try to use the public link to view plain jbrowse, there is nothing but a
white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are not allowed by
this realm.
I have also tried to use 2.0.2 with similar results - blank white screen
where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to
download. The directory "jbrowse-download" has the plugins directory but no
other jbrowse directory. I have downloaded Jbrowse and manually copied the
contents of the Jbrowse file into the "jbrowse-download" directory but I
still get a white screen in the jbrowse pane of webapollo. I have tried
this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6,
and 1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running into the
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
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
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
| 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/
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

[Loraine Guéguen]

Hi Nathan,

To let you know what we did :
We finally installed version 2.0.2 with git, but because we were not
able to get the JBrowse with clean-all, rm and deploy (empty
jbrowse-download directory), we copied the content of the
jbrowse-download directory obtained from the apollo tar.gz archive.

Maybe this issue is solved in the 2.0.3.
Thanks

Loraine Guéguen

Post by Nathan Dunn
JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse.
Sometimes github get stuck and the process needs to start over (this
is vastly improved in the master branch, which will become 2.0.3).
I would recommend the 2.0.2 version.
To “unstick it” you have to clean JBrowse as well, which is what
clean-all does (“./apollo clean-all ; ./apollo deploy”). Conversely
you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and
then build, but clean-all is a better way. After you type “./apollo
deploy” please verify that your jbrowse-download/src is there with
multiple directories fully populated (you should see a “main.js” in
the directories).
I think that will fix both problems (the null usernames might just
indicate that you have not registered a user or logged in).
Please post the full logs (clean and build) if anything goes wrong so
I can determine if there is anything else going on.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Post by Loraine Guéguen
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are
empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen

Post by Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left
menu pain but the Jbrowse pane is white
"org.apache.shiro.authc.AccountException: Null usernames are not
allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded
with the deploy script, contrary to version 2.0.2), with a postgres
database.
Thank you in advance,
Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as
well as the directory that tomcat creates when it deploys a new war
file. I also delete the directory under
tomcat/work/Catalina/localhost (although I don't know if this is
necessary). I did have older versions of WebApollo in tomcat so I
removed them also. I get the same errors listed above. I am using
version 2.0.1 at this time because Jbrowse seems to download when
running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the
downloads on the source page
(https://github.com/GMOD/Apollo/releases)? If its the former
you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove
everything related to apollo from your tomcat webapps
directory. e.g., typically the apollo.war file will explode
its contents into a directory called “apollo” in the webapps
directory. You should remove that directory when you upgrade
as you might have stale javascript and other files in there
that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some
problems. The annotator would work for one browse but
subsequent attempts to log in would not work. The catalina
output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo
and I can see the left menu pain but the the Jbrowse pane is
white. I can even see the reference sequence in the WebApollo
menu tab "Ref Sequence" after I load a sequence but there are
no tracks listed in the "Tracks" tab. When I try to use the
public link to view plain jbrowse, there is nothing but a
white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are
not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank
white screen where jbrowse panel should be while the WebApollo
panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not
seem to download. The directory "jbrowse-download" has the
plugins directory but no other jbrowse directory. I have
downloaded Jbrowse and manually copied the contents of the
Jbrowse file into the "jbrowse-download" directory but I still
get a white screen in the jbrowse pane of webapollo. I have
tried this with the following versions of Jbrowse with no
luck: 1.11.5, 1.11.6, and 1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
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
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
subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
This list is for the Apollo Annotation Editing Tool. Info athttp://genomearchitect.org/

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
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
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/

[Nathan Dunn]

It should be significantly better with the 2.0.3 release (which is released): https://github.com/GMOD/Apollo/tree/2.0.3 <https://github.com/GMOD/Apollo/tree/2.0.3>

The only caveat is you need to install node.js and bower (npm install -g bower), but I haven’t run into any further git clone issues with JBrowse since.

Please let me know if you run into any issues.

Nathan

Post by Nathan Henry
Hi Nathan,
We finally installed version 2.0.2 with git, but because we were not able to get the JBrowse with clean-all, rm and deploy (empty jbrowse-download directory), we copied the content of the jbrowse-download directory obtained from the apollo tar.gz archive.
Maybe this issue is solved in the 2.0.3.
Thanks
Loraine Guéguen

Post by Nathan Dunn
JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse. Sometimes github get stuck and the process needs to start over (this is vastly improved in the master branch, which will become 2.0.3). I would recommend the 2.0.2 version.
To “unstick it” you have to clean JBrowse as well, which is what clean-all does (“./apollo clean-all ; ./apollo deploy”). Conversely you can do a “rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but clean-all is a better way. After you type “./apollo deploy” please verify that your jbrowse-download/src is there with multiple directories fully populated (you should see a “main.js” in the directories).
I think that will fix both problems (the null usernames might just indicate that you have not registered a user or logged in).
Please post the full logs (clean and build) if anything goes wrong so I can determine if there is anything else going on.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Post by Loraine Guéguen
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen

Post by Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the downloads on the source page (https://github.com/GMOD/Apollo/releases <https://github.com/GMOD/Apollo/releases>)? If its the former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory. e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory. You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
<>
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.
https://github.com/GMOD/Apollo/issues/555 <https://github.com/GMOD/Apollo/issues/555>
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at <http://genomearchitect.org/>http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Henry]

Hi Loraine,

Thanks for lettings us know!

Henry

Post by Nathan Dunn
It should be significantly better with the 2.0.3 release (which is
released): https://github.com/GMOD/Apollo/tree/2.0.3
The only caveat is you need to install node.js and bower (npm install -g
bower), but I haven’t run into any further git clone issues with JBrowse
since.
Please let me know if you run into any issues.
Nathan
Hi Nathan,
We finally installed version 2.0.2 with git, but because we were not able
to get the JBrowse with clean-all, rm and deploy (empty jbrowse-download
directory), we copied the content of the jbrowse-download directory
obtained from the apollo tar.gz archive.
Maybe this issue is solved in the 2.0.3.
Thanks
Loraine Guéguen
JBrowse 2.0.1 and 2.0.2 use git (and GitHub) to build JBrowse. Sometimes
github get stuck and the process needs to start over (this is vastly
improved in the master branch, which will become 2.0.3). I would
recommend the 2.0.2 version.
To “unstick it” you have to clean JBrowse as well, which is what clean-all
does (“./apollo clean-all ; ./apollo deploy”). Conversely you can do a
“rm -rf jbrowse-download ; rm -rf web-app/jbrowse” and then build, but
clean-all is a better way. After you type “./apollo deploy” please verify
that your jbrowse-download/src is there with multiple directories fully
populated (you should see a “main.js” in the directories).
I think that will fix both problems (the null usernames might just
indicate that you have not registered a user or logged in).
Please post the full logs (clean and build) if anything goes wrong so I
can determine if there is anything else going on.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are empty
after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu
pain but the Jbrowse pane is white
Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the
deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as
the directory that tomcat creates when it deploys a new war file. I also
delete the directory under tomcat/work/Catalina/localhost (although I don't
know if this is necessary). I did have older versions of WebApollo in
tomcat so I removed them also. I get the same errors listed above. I am
using version 2.0.1 at this time because Jbrowse seems to download when
running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry

Post by Nathan Dunn
Also, are you upgrading directly from git or are you uses the downloads
on the source page (https://github.com/GMOD/Apollo/releases)? If its
the former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything
related to apollo from your tomcat webapps directory. e.g., typically the
apollo.war file will explode its contents into a directory called “apollo”
in the webapps directory. You should remove that directory when you
upgrade as you might have stale javascript and other files in there that
might cause problems.
Nathan
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems.
The annotator would work for one browse but subsequent attempts to log in
would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can
see the left menu pain but the the Jbrowse pane is white. I can even see
the reference sequence in the WebApollo menu tab "Ref Sequence" after I
load a sequence but there are no tracks listed in the "Tracks" tab. When I
try to use the public link to view plain jbrowse, there is nothing but a
white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR
org.apache.shiro.authc.AccountException: Null usernames are not allowed by
this realm.
I have also tried to use 2.0.2 with similar results - blank white screen
where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to
download. The directory "jbrowse-download" has the plugins directory but no
other jbrowse directory. I have downloaded Jbrowse and manually copied the
contents of the Jbrowse file into the "jbrowse-download" directory but I
still get a white screen in the jbrowse pane of webapollo. I have tried
this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6,
and 1.12.1.
I eventually reverted back to 2.0.0 but I believe I am running into the
https://github.com/GMOD/Apollo/issues/555
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at
<http://genomearchitect.org/>http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with
| 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
unsubscribe apollo | 3. Leave the message body blank.

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
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
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[Nathan Dunn]

Loraine,

I think that Nathan (the other one) stuck with 2.0.0.

However, if there are ways we could improve the build in 2.0.3, the Apollo team would definitely like to know.

Nathan

Post by Loraine Guéguen
Hi again,
I have just seen that some repositories in jbrowse-download/src/ are empty after clean-all and then deploy (e.g. dojo, dojox, util, dbind).
Any idea why and how to solve that ?
Thanks
Loraine Guéguen

Post by Loraine Guéguen
Hi Henry,
Did you solve your problem ?
We have the same issues : log into WebApollo and can see the left menu pain but the Jbrowse pane is white
And error in the catalina logs : "org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm"
We are using version 2.0.1 as well (because Jbrowse is downloaded with the deploy script, contrary to version 2.0.2), with a postgres database.
Thank you in advance,
Loraine Guéguen

Post by Nathan Henry
Hi Nathan,
I am downloading the tar.gz from the releases page.
Before I deploy to tomcat I delete the war file I am replacing as well as the directory that tomcat creates when it deploys a new war file. I also delete the directory under tomcat/work/Catalina/localhost (although I don't know if this is necessary). I did have older versions of WebApollo in tomcat so I removed them also. I get the same errors listed above. I am using version 2.0.1 at this time because Jbrowse seems to download when running the deploy script for this version.
Do you have other suggestions?
Thank you for your time,
Henry
Also, are you upgrading directly from git or are you uses the downloads on the source page ( <https://github.com/GMOD/Apollo/releases>https://github.com/GMOD/Apollo/releases <https://github.com/GMOD/Apollo/releases>)? If its the former you’ll want to do a “./apollo clean-all” before you rebuild.
In either case, when you do your upgrade, you should remove everything related to apollo from your tomcat webapps directory. e.g., typically the apollo.war file will explode its contents into a directory called “apollo” in the webapps directory. You should remove that directory when you upgrade as you might have stale javascript and other files in there that might cause problems.
Nathan

Post by Nathan Henry
Hi,
I have some issues with 2.0.1 and 2.0.2.
I attempted to upgrade from 2.0.0 to 2.0.2 but ran into some problems. The annotator would work for one browse but subsequent attempts to log in would not work. The catalina output had a lot of data about broken pipes.
I have tried to isntall 2.0.1 from scratch.
The WebApollo part of the app works. I can log into WebApollo and I can see the left menu pain but the the Jbrowse pane is white. I can even see the reference sequence in the WebApollo menu tab "Ref Sequence" after I load a sequence but there are no tracks listed in the "Tracks" tab. When I try to use the public link to view plain jbrowse, there is nothing but a white screen.
ReferenceError: require is not defined
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
<>
2016-05-04 16:04:04,288 [http-bio-8080-exec-5] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
I have also tried to use 2.0.2 with similar results - blank white screen where jbrowse panel should be while the WebApollo panels work.
Also, when run ./apollo deploy with 2.0.2 Jbrowse does not seem to download. The directory "jbrowse-download" has the plugins directory but no other jbrowse directory. I have downloaded Jbrowse and manually copied the contents of the Jbrowse file into the "jbrowse-download" directory but I still get a white screen in the jbrowse pane of webapollo. I have tried this with the following versions of Jbrowse with no luck: 1.11.5, 1.11.6, and 1.12.1.
https://github.com/GMOD/Apollo/issues/555 <https://github.com/GMOD/Apollo/issues/555>
I am using postgres 9.3 as my database.
Does anyone have any suggestions?
Thanks for your time,
Henry
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/