Sequence Alignment servers greyed out?

Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

···

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

Hi Mark.

Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

We upgraded JABAWS last week, at the same time as releasing v2.8.1. We didn't expect this to cause any problems - since our tests showed that v2.1 works with Jalview 2.7 onwards (and most likely, 2.6 onwards, too). However, there may be issues with java versions on different platforms.

Could you follow the faq (http://www.jalview.org/faq#bug) and send me your Jalview console log output ?

Thanks!
Jim.

···

On Wed Jun 11 21:30:41 2014, Mark A Saper wrote:

Jim,

I traced the problem to my jalview.jlnp file that I use to launch jalview. Although Java downloaded the new jalview 2.8.1 I continued to launch jalview with a jalview.jnlp file that I have in my /Applications folder which had reference to the older version of JABAWS. This has happened several times before over the years. How can always launch the program with the most recent jalview? Use a link?

My platform is OS X 10.8.5 running Oracle Java 1.7.0_60.

Regards, Mark

software that I am running is 2.8.1

···

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 2:06 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi Mark.

On Wed Jun 11 21:30:41 2014, Mark A Saper wrote:
Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

We upgraded JABAWS last week, at the same time as releasing v2.8.1. We didn't expect this to cause any problems - since our tests showed that v2.1 works with Jalview 2.7 onwards (and most likely, 2.6 onwards, too). However, there may be issues with java versions on different platforms.

Could you follow the faq (http://www.jalview.org/faq#bug) and send me your Jalview console log output ?

Thanks!
Jim.

Hi Mark.

I traced the problem to my jalview.jlnp file that I use to launch jalview. Although Java downloaded the new jalview 2.8.1 I continued to launch jalview with a jalview.jnlp file that I have in my /Applications folder which had reference to the older version of JABAWS.

Well done for working that out !

   This has happened several times before over the years. How can always launch the program with the most recent jalview? Use a link?

That's a good question. We could change the way we distribute the code so the jnlp file just contains a reference to one (or two) stable jar files that contain all the other dependencies.. this would mean that once you had configured your favourite JNLP once, it would work for all future versions regardless of dependency changes. The downside of that is that it is a fairly large single file download.

I'll raise a feature request about this and get back to you - we plan to change the way the desktop is launched in the next 6 months or so, which should get around all these problems, but if you want to hear about when we do something about it sooner, then hit the 'watch' button on the issue (http://issues.jalview.org/browse/JAL-1525).

Once again, thanks for taking the time to work out what was going wrong ! In principle, Java should actually have prevented Jalview from launching because the default security settings do not allow applications to be launched from a JNLP that doesn't match the version shipped with the application (e.g. one that has different dependencies).. but that would have been just as annoying, I guess.

Cheers,
Jim

···

On 12/06/2014 14:30, Mark A Saper wrote:

Hi Jim,

I figured out the right way to launch Jalview in OS X. This assumes you have Oracle Java 1.7 installed and have already run and downloaded jalview.

1. In System Preferences, launch Java which opens Java Control Panel.
2. On the "General" pane, click "View..." which opens Java Cache Viewer
3. Select Jalview
4. Click icon for creating a shortcut. A Mac alias is installed on your Desktop. Drag it /Applications or wherever you want it.
5. Double-click the Jalview alias file to launch.

The first time it will download all of the jalview objects into cache again. Subsequent launches will only check for any updates, then launch.

-Mark

···

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 9:30 AM, Mark A Saper <saper@umich.edu> wrote:

Jim,

I traced the problem to my jalview.jlnp file that I use to launch jalview. Although Java downloaded the new jalview 2.8.1 I continued to launch jalview with a jalview.jnlp file that I have in my /Applications folder which had reference to the older version of JABAWS. This has happened several times before over the years. How can always launch the program with the most recent jalview? Use a link?

My platform is OS X 10.8.5 running Oracle Java 1.7.0_60.

Regards, Mark

software that I am running is 2.8.1
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 2:06 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi Mark.

On Wed Jun 11 21:30:41 2014, Mark A Saper wrote:
Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

We upgraded JABAWS last week, at the same time as releasing v2.8.1. We didn't expect this to cause any problems - since our tests showed that v2.1 works with Jalview 2.7 onwards (and most likely, 2.6 onwards, too). However, there may be issues with java versions on different platforms.

Could you follow the faq (http://www.jalview.org/faq#bug) and send me your Jalview console log output ?

Thanks!
Jim.

Thanks for this Mark - we'll add these instructions to our website.

Windows will automatically create an icon for the JNLP file after you launch it a few times, but that mechanism seems broken in OSX. I'm glad you found a way to do this manually!

Jim.
ps. I'm still not sure this mechanism will cope with the case when the libraries in the JNLP file change.. but I'll check it when I come to make the next release.

···

On Thu Jun 12 15:34:25 2014, Mark A Saper wrote:

Hi Jim,

I figured out the right way to launch Jalview in OS X. This assumes you have Oracle Java 1.7 installed and have already run and downloaded jalview.

1. In System Preferences, launch Java which opens Java Control Panel.
2. On the "General" pane, click "View..." which opens Java Cache Viewer
3. Select Jalview
4. Click icon for creating a shortcut. A Mac alias is installed on your Desktop. Drag it /Applications or wherever you want it.
5. Double-click the Jalview alias file to launch.

The first time it will download all of the jalview objects into cache again. Subsequent launches will only check for any updates, then launch.

-Mark

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 9:30 AM, Mark A Saper <saper@umich.edu> wrote:

Jim,

I traced the problem to my jalview.jlnp file that I use to launch jalview. Although Java downloaded the new jalview 2.8.1 I continued to launch jalview with a jalview.jnlp file that I have in my /Applications folder which had reference to the older version of JABAWS. This has happened several times before over the years. How can always launch the program with the most recent jalview? Use a link?

My platform is OS X 10.8.5 running Oracle Java 1.7.0_60.

Regards, Mark

software that I am running is 2.8.1
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 2:06 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi Mark.

On Wed Jun 11 21:30:41 2014, Mark A Saper wrote:
Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

We upgraded JABAWS last week, at the same time as releasing v2.8.1. We didn't expect this to cause any problems - since our tests showed that v2.1 works with Jalview 2.7 onwards (and most likely, 2.6 onwards, too). However, there may be issues with java versions on different platforms.

Could you follow the faq (http://www.jalview.org/faq#bug) and send me your Jalview console log output ?

Thanks!
Jim.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Jim,

I actually think Jalview creates the icon automatically, as it reappears on the Desktop if I delete it.

I may have a similar problem later if things change again.

···

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 11:58 AM, Jim Procter <foreveremain@gmail.com> wrote:

Thanks for this Mark - we'll add these instructions to our website.

Windows will automatically create an icon for the JNLP file after you launch it a few times, but that mechanism seems broken in OSX. I'm glad you found a way to do this manually!

Jim.
ps. I'm still not sure this mechanism will cope with the case when the libraries in the JNLP file change.. but I'll check it when I come to make the next release.

On Thu Jun 12 15:34:25 2014, Mark A Saper wrote:

Hi Jim,

I figured out the right way to launch Jalview in OS X. This assumes you have Oracle Java 1.7 installed and have already run and downloaded jalview.

1. In System Preferences, launch Java which opens Java Control Panel.
2. On the "General" pane, click "View..." which opens Java Cache Viewer
3. Select Jalview
4. Click icon for creating a shortcut. A Mac alias is installed on your Desktop. Drag it /Applications or wherever you want it.
5. Double-click the Jalview alias file to launch.

The first time it will download all of the jalview objects into cache again. Subsequent launches will only check for any updates, then launch.

-Mark

_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 9:30 AM, Mark A Saper <saper@umich.edu> wrote:

Jim,

I traced the problem to my jalview.jlnp file that I use to launch jalview. Although Java downloaded the new jalview 2.8.1 I continued to launch jalview with a jalview.jnlp file that I have in my /Applications folder which had reference to the older version of JABAWS. This has happened several times before over the years. How can always launch the program with the most recent jalview? Use a link?

My platform is OS X 10.8.5 running Oracle Java 1.7.0_60.

Regards, Mark

software that I am running is 2.8.1
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

On Jun 12, 2014, at 2:06 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi Mark.

On Wed Jun 11 21:30:41 2014, Mark A Saper wrote:
Is JABAWS available? A couple of days ago the Sequence alignment services became "greyed" out.

We upgraded JABAWS last week, at the same time as releasing v2.8.1. We didn't expect this to cause any problems - since our tests showed that v2.1 works with Jalview 2.7 onwards (and most likely, 2.6 onwards, too). However, there may be issues with java versions on different platforms.

Could you follow the faq (http://www.jalview.org/faq#bug) and send me your Jalview console log output ?

Thanks!
Jim.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss