install4j

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JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/... This is better in multiple ways including collating files needed for the hugo website and website docroot.

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Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

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JAL-3393 Updated DS_Store files, script and doc

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JAL-3393 improved flexibility of script and updated doc

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JAL-3393 Made an all-in-one script to create the DS_Store from scratch (has to be run on a mac desktop, it incorporates the AppleScript Finder adjustments). Updated docs. Updated the release DMG background image with the script. Changed install4j9 to put the background image as .background/background.png.

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    ./set_relative_dmg_background_image.applescript
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JAL-3393 Added version number to DMG Volume name. New jalview_dmg_DS_Store and documentation about it

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    ./set_relative_dmg_background_image.applescript
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JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

JAL-3962 Added jre/bin and dist folders to the native library path to try and fix the awt.dll problem

JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
JAL-3830 JAL-3420 added new jvl_file to install4j9 template

new jvl_file svg, png, ico and icns files, and changed references to Jalview-Launch to jvl_file

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    ./file_associations_auto-Info_plist.xml
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    ./file_associations_auto-install4j8.xml
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    ./file_associations_auto-install4j8.xml
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    ./file_associations_template-install4j8.xml
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    ./file_associations_auto-install4j8.xml
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    ./file_associations_template-install4j8.xml
JAL-3553 now creating a json file for use on website. It's easier to parse all the info here than on the website!

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JAL-3553 added customized labels for install4j output.txt

JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt

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JAL-3830 forgot to uncheck this

JAL-3830 polished setup app for macos

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JAL-3830 quick fix to installer text

JAL-3830 install4j9 tries to parse and can't cope with the hyphens and filename format of the jre-VERSION-OS-ARCH.tar.gz JRE tar files, so using underscores in symbolic links

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JAL-3830 Added steps for install4j9 to create macOS symbolic link to wrapper script (link) at /Applications/Jalview.app/Contents/MacOS/jalview and to add icon to Dock

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    ./install4j9_template.install4j
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JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

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    ./README-DMG_background_image_creation.md
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    ./README_convert_PNG_to_ICNS_and_ICO
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JAL-3594 Changed logo for Jalview Test

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JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer.

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    ./file_associations_auto-Info_plist.xml
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    ./file_associations_auto-install4j8.xml
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JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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JAL-3830 delete channel.props and channel.propsv when uninstalling

JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

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JAL-3830 add the windows bash script to getdown files and install4j installers

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