InstallAnywhere

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JAL-3474 removed all .cvsignore files stored in the repo

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JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar

JAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete

  1. … 1 more file in changeset.
JAL-3111 biojava dependencies

JAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere

JAL-3111 fix jabaws dependency name in IA config

JAL-3111 intervalstore library on IA classpath

JAL-3111 typo in IA config

JAL-3111 update InstallAnywhere dependencies for changed libraries

JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar

  1. … 5 more files in changeset.
JAL-3101 increase default heap size in IA and JNLP generation, and generate a jalview_256MB.jnlp file for backwards compatibility

  1. … 1 more file in changeset.
JAL-2988 update InstallAnywhere install dependencies for VAqua5

JAL-3065 - amended commit 4906697ab6e5a79fbce3baae89f7f64178c9a739 to exclude .settings/..groovy Added notes to the instructions, also adjusted the jalviewDesktopRunner test to lookup OS and use ';' or ':' accordingly. All the CommandLineOperations tests failed on my (hastily set up) linux box, so I'm committing and will test on MacOS too.

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should really explain what path to classes is as well as path to lib here

should really explain what path to classes is as well as path to lib here

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

JAL-3065

Change in all repo documentation advising launching Jalview with the

-Djava.ext.dirs=LIB

option to now use

-classpath="LIB/*:..."

instead. Using the -Djava.ext.dirs= option masks the JRE's own ext dir

which contains the sunjce packages. This manifests as cipher problems

when accessing https resources (in particular https://www.ebi.ac.uk/...

when searching for PDB structures, activated when choosing Sequence->"3D

Structure Data...")

  1. … 4 more files in changeset.
JAL-2931 patch IA paths for new build box

JAL-2976 typo in installAnywhere build for VAqua dependency

JAL-2976 Vaqua(4) as a dependency

  1. … 3 more files in changeset.
JAL-2069 spike updated with latest (FeatureTypeSettings)

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JAL-2698 only allow InstallAnywhere launches with version 1.8.* of java - java 9 JVM args not yet working for 2.10.3

JAL-2698 patch path for InstallAnywhere build. Webstart and source builds unchanged

JAL-2738 copy to spikes/mungo

  1. … 568 more files in changeset.
JAL-2675 update destination jar name of min-jabaws-client to 2.2

spike branch updated from latest features/JAL-2446

  1. … 86 more files in changeset.
JAL-2606 updated IA build for changed dependency due to JAL-2549

JAL-2325 JAL-1878 update minimum versions of JRE for running/installing on windows and OSX

JAL-2325 JAL-2273 update vms bound to different installers