display problems

Jalview Discussion
1

Dear, I have installed jalview version 2.11.1.4 and when I start it from phytozome the alignment is not displayed correctly. The following image appears

imagen.png
imagen.png1108×625 23.4 KB

I have defined the openjdk 11 version as the default java as below, but the result is the same

INSTALL4J_JAVA_HOME_OVERRIDE = / usr / lib / jvm / java-11-openjdk-amd64 / bin / java ~ / opt / Jalview / Jalview

Could you help me?

Thanks!

···

Dr. Mariano Pardo
Sección Biotecnología
Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA),
Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo
Nacional de Investigaciones Científicas y Técnicas (CONICET)
Av. William Cross 3150 - C.P. T4101XAC
Las Talitas - Tucumán - Argentina
Tel: (54 - 381) 452 1000 (200)

2

Hi Mariano (posting to the list as well this time !)

Thanks for mailing jalview-discuss !

It looks as if Phytozome launches their own custom version of Jalview - since there is a old-style Java JNLP launch file shown in the alignment window.

There are a couple of ways you can resolve this - either manually import the data from the phytozome web site into Jalview, or you can open the /tmp/mozilla_mariano0/jalview-3.jnlp file in a text editor and copy out the arguments that the phytozome site was trying to pass using the JNLP file. The second one is pretty easy:

Open the jnlp file in a text editor, and look for elements. Assuming you have ‘jalview’ on your path, copy and paste them into a terminal as arguments for the jalview command:
e.g.
-open
https://phytozome.jgi.doe.gov/cgi-bin/getClusterSeq?transcript[]=33081360&members=0&db=Phytozome&seqtype=p&exclude=-1&file=0&centroid=0&def=1

becomes:
jalview -open ‘https://phytozome.jgi.doe.gov/cgi-bin/getClusterSeq?transcript[]=33081360&members=0&db=Phytozome&seqtype=p&exclude=-1&file=0&centroid=0&def=1’

(that’s all one line by the way)

In this case, the URL from phytozome can also be imported directly via Archivo-> Alineamiento de entrada → Alineamiento de entrada desde URL

Let us know how you get on ! We’ll see if we can get in contact with the Phytozome maintainers and ask them to update their Launch Jalview button too.

Jim.

imagen.png
imagen.png1108×625 23.4 KB

···

On Tue, 6 Jul 2021 at 16:38, Mariano Pardo <mpardokarate@gmail.com> wrote:

Dear, I have installed jalview version 2.11.1.4 and when I start it from phytozome the alignment is not displayed correctly. The following image appears

imagen.png

I have defined the openjdk 11 version as the default java as below, but the result is the same

INSTALL4J_JAVA_HOME_OVERRIDE = / usr / lib / jvm / java-11-openjdk-amd64 / bin / java ~ / opt / Jalview / Jalview

Could you help me?

Thanks!

–

Dr. Mariano Pardo
Sección Biotecnología
Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA),
Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo
Nacional de Investigaciones Científicas y Técnicas (CONICET)
Av. William Cross 3150 - C.P. T4101XAC
Las Talitas - Tucumán - Argentina
Tel: (54 - 381) 452 1000 (200)

–

Dr. Mariano Pardo
Sección Biotecnología
Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA),
Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo
Nacional de Investigaciones Científicas y Técnicas (CONICET)
Av. William Cross 3150 - C.P. T4101XAC
Las Talitas - Tucumán - Argentina
Tel: (54 - 381) 452 1000 (200)

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