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 <argument></argument> elements. Assuming you have 'jalview' on your path, copy and paste them into a terminal as arguments for the jalview command: e.g. <argument>-open</argument> <argument> https://phytozome.jgi.doe.gov/cgi-bin/getClusterSeq?transcript[]=33081360&members=0&db=Phytozome&seqtype=p&exclude=-1&file=0¢roid=0&def=1 </argument> becomes: jalview -open ' https://phytozome.jgi.doe.gov/cgi-bin/getClusterSeq?transcript[]=33081360&members=0&db=Phytozome&seqtype=p&exclude=-1&file=0¢roid=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. On Tue, 6 Jul 2021 at 16:38, Mariano Pardo <[email protected]> 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 > > [image: 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) > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >
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