bump to 2.11.1.4 change source

5 files changed, 36 insertions, 588 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 91b42fb75741..fdfc4f1a9a12 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,170 +1,18 @@
 pkgbase = jalview
 	pkgdesc = Bioinformatics Multiple Alignment Editor
-	pkgver = 2.11.0
-	pkgrel = 2
+	pkgver = 2.11.1.4
+	pkgrel = 1
 	url = https://www.jalview.org/
 	arch = any
 	license = GPL3
 	depends = java-runtime
-	noextract = jalview.jar
-	noextract = JGoogleAnalytics_0.3.jar
-	noextract = Jmol-14.6.4_2016.10.26.jar
-	noextract = VARNAv3-93.jar
-	noextract = VAqua5-patch.jar
-	noextract = activation.jar
-	noextract = apache-mime4j-0.6.jar
-	noextract = axis.jar
-	noextract = biojava-core-4.1.0.jar
-	noextract = biojava-ontology-4.1.0.jar
-	noextract = castor-1.1-cycle-xml.jar
-	noextract = commons-codec-1.3.jar
-	noextract = commons-discovery.jar
-	noextract = commons-logging-1.1.1.jar
-	noextract = groovy-all-2.4.12-indy.jar
-	noextract = htsjdk-1.133.jar
-	noextract = httpclient-4.0.3.jar
-	noextract = httpcore-4.0.1.jar
-	noextract = httpmime-4.0.3.jar
-	noextract = jabaws-min-client-2.2.0.jar
-	noextract = jalview_jnlp_vm.jar
-	noextract = java-json.jar
-	noextract = jaxrpc.jar
-	noextract = jdas-1.0.4.jar
-	noextract = jersey-client-1.19.jar
-	noextract = jersey-core-1.19.jar
-	noextract = jersey-json-1.19.jar
-	noextract = jetty-http-9.2.10.v20150310.jar
-	noextract = jetty-io-9.2.10.v20150310.jar
-	noextract = jetty-server-9.2.10.v20150310.jar
-	noextract = jetty-util-9.2.10.v20150310.jar
-	noextract = jfreesvg-2.1.jar
-	noextract = jhall.jar
-	noextract = json_simple-1.1.jar
-	noextract = jsoup-1.8.1.jar
-	noextract = jsr311-api-1.1.1.jar
-	noextract = jswingreader-0.3.jar
-	noextract = log4j-to-slf4j-2.0-rc2.jar
-	noextract = mail.jar
-	noextract = miglayout-4.0-swing.jar
-	noextract = regex.jar
-	noextract = saaj.jar
-	noextract = servlet-api-3.1.jar
-	noextract = slf4j-api-1.7.7.jar
-	noextract = slf4j-log4j12-1.7.7.jar
-	noextract = spring-core-3.0.5.RELEASE.jar
-	noextract = spring-web-3.0.5.RELEASE.jar
-	noextract = vamsas-client.jar
-	noextract = wsdl4j.jar
-	noextract = xercesImpl.jar
-	noextract = xml-apis.jar
-	source = https://www.jalview.org/webstart/jalview.jar
-	source = https://www.jalview.org/webstart/JGoogleAnalytics_0.3.jar
-	source = https://www.jalview.org/webstart/Jmol-14.6.4_2016.10.26.jar
-	source = https://www.jalview.org/webstart/VARNAv3-93.jar
-	source = https://www.jalview.org/webstart/VAqua5-patch.jar
-	source = https://www.jalview.org/webstart/activation.jar
-	source = https://www.jalview.org/webstart/apache-mime4j-0.6.jar
-	source = https://www.jalview.org/webstart/axis.jar
-	source = https://www.jalview.org/webstart/biojava-core-4.1.0.jar
-	source = https://www.jalview.org/webstart/biojava-ontology-4.1.0.jar
-	source = https://www.jalview.org/webstart/castor-1.1-cycle-xml.jar
-	source = https://www.jalview.org/webstart/commons-codec-1.3.jar
-	source = https://www.jalview.org/webstart/commons-discovery.jar
-	source = https://www.jalview.org/webstart/commons-logging-1.1.1.jar
-	source = https://www.jalview.org/webstart/groovy-all-2.4.12-indy.jar
-	source = https://www.jalview.org/webstart/htsjdk-1.133.jar
-	source = https://www.jalview.org/webstart/httpclient-4.0.3.jar
-	source = https://www.jalview.org/webstart/httpcore-4.0.1.jar
-	source = https://www.jalview.org/webstart/httpmime-4.0.3.jar
-	source = https://www.jalview.org/webstart/jabaws-min-client-2.2.0.jar
-	source = https://www.jalview.org/webstart/jalview_jnlp_vm.jar
-	source = https://www.jalview.org/webstart/java-json.jar
-	source = https://www.jalview.org/webstart/jaxrpc.jar
-	source = https://www.jalview.org/webstart/jdas-1.0.4.jar
-	source = https://www.jalview.org/webstart/jersey-client-1.19.jar
-	source = https://www.jalview.org/webstart/jersey-core-1.19.jar
-	source = https://www.jalview.org/webstart/jersey-json-1.19.jar
-	source = https://www.jalview.org/webstart/jetty-http-9.2.10.v20150310.jar
-	source = https://www.jalview.org/webstart/jetty-io-9.2.10.v20150310.jar
-	source = https://www.jalview.org/webstart/jetty-server-9.2.10.v20150310.jar
-	source = https://www.jalview.org/webstart/jetty-util-9.2.10.v20150310.jar
-	source = https://www.jalview.org/webstart/jfreesvg-2.1.jar
-	source = https://www.jalview.org/webstart/jhall.jar
-	source = https://www.jalview.org/webstart/json_simple-1.1.jar
-	source = https://www.jalview.org/webstart/jsoup-1.8.1.jar
-	source = https://www.jalview.org/webstart/jsr311-api-1.1.1.jar
-	source = https://www.jalview.org/webstart/jswingreader-0.3.jar
-	source = https://www.jalview.org/webstart/log4j-to-slf4j-2.0-rc2.jar
-	source = https://www.jalview.org/webstart/mail.jar
-	source = https://www.jalview.org/webstart/miglayout-4.0-swing.jar
-	source = https://www.jalview.org/webstart/regex.jar
-	source = https://www.jalview.org/webstart/saaj.jar
-	source = https://www.jalview.org/webstart/servlet-api-3.1.jar
-	source = https://www.jalview.org/webstart/slf4j-api-1.7.7.jar
-	source = https://www.jalview.org/webstart/slf4j-log4j12-1.7.7.jar
-	source = https://www.jalview.org/webstart/spring-core-3.0.5.RELEASE.jar
-	source = https://www.jalview.org/webstart/spring-web-3.0.5.RELEASE.jar
-	source = https://www.jalview.org/webstart/vamsas-client.jar
-	source = https://www.jalview.org/webstart/wsdl4j.jar
-	source = https://www.jalview.org/webstart/xercesImpl.jar
-	source = https://www.jalview.org/webstart/xml-apis.jar
-	source = logo.gif
+	noextract = jalview-2_11_1_4-unix-java_8.tar.gz
+	source = http://www.jalview.org/getdown/release/install4j/1.8/jalview-2_11_1_4-unix-java_8.tar.gz
 	source = jalview
 	source = jalview.desktop
-	sha256sums = c503c683d18750a08490ad9eec7e18877d752ae8ca7607c70e021cc4c0acf671
-	sha256sums = 9e34f0f3b6fb78b07b20b354548ee2ae491e34a0b7dc387c303e20c6f1698fae
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-	sha256sums = 8559555902a4dcb07a1399a7f689116bd42e1a804b8f256aea44497d157b2369
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-	sha256sums = a8e308ed218978fc77aed03c0d504e4634014e46f0817575977c9523e3f188fc
-	sha256sums = 1e4434bc5025dc73a084b278b53d5820dc61e471e88f48e31fec65eed430c910
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-	sha256sums = d09d653869ce8d653cb96b865523b4ece48ec35d341f987d9b02a027507a3400
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-	sha256sums = ade0c607d1d6313d2381523ce965391369736ba5d80c0603a7bde3df08d30bb6
-	sha256sums = e3f0bb4626475674428ab64c864ec48b43d01620aebcdcc3e58ac248d0acde8e
-	sha256sums = 49c785261ee701eec7c6b7d4b2839077d52b2b668de0a4298f0848d89ef5cd0d
-	sha256sums = 362790ef6d3e3c537a6d31663a0e7f3ec9664c90cb9dc6df4a80b016f474eaa4
-	sha256sums = d5d4f97f520d58ddb8f2552800f946c2ab6c89c3dd105b7a9cd777b9925bc17e
-	sha256sums = 4c87a84ec39e677fe2922a5e78cf68cf508ec8dff5211193b11aac7cb1cf4211
+	sha256sums = 32fa6106f3afedf7e60d4b1c8006846903e4cdaa0730190cfea399ab49202c05
+	sha256sums = dbe5edfa9b17a1f85083b5aae16ef7a186a0d0035e6a81761cf73d0e1121ce58
+	sha256sums = d9e0823d3b724d1c373763864d5daf6ebd59d1511347ec461310324afa45448e
 
 pkgname = jalview
 
diff --git a/.gitignore b/.gitignore
index 1a1759ec34ca..f720d3781b62 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,240 +1,6 @@
-*.pkg.tar.*
-*.jar
-jalview.jnlp
-pkg
-src
-
-### https://raw.github.com/github/gitignore/0c5ace9de99c220bb69012581d68ca6fa977449b/Python.gitignore
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-.static_storage/
-.media/
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-
-### https://raw.github.com/github/gitignore/0c5ace9de99c220bb69012581d68ca6fa977449b/Python.gitignore
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-.static_storage/
-.media/
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-
-### https://raw.github.com/github/gitignore/0c5ace9de99c220bb69012581d68ca6fa977449b/Global/Vim.gitignore
-
-# Swap
-[._]*.s[a-v][a-z]
-[._]*.sw[a-p]
-[._]s[a-v][a-z]
-[._]sw[a-p]
-
-# Session
-Session.vim
-
-# Temporary
-.netrwhist
-*~
-# Auto-generated tag files
-tags
-
-
+*
+!PKGBUILD
+!.SRCINFO
+!.gitignore
+!.desktop
+!jalview
diff --git a/PKGBUILD b/PKGBUILD
index f0fe2c8a035b..17c3ae3db94b 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,199 +1,34 @@
-# Maintainer:
+# Maintainer: PumpkinCheshire <sollyonzou at gmail dot com>
 # Contributor: Felix Golatofski <contact@xdfr.de>
 # Contributor: Stefan Seemayer <mail@semicolonsoftware.de>
 
 pkgname=jalview
-pkgver=2.11.0
-pkgrel=2
+pkgver=2.11.1.4
+pkgrel=1
 pkgdesc="Bioinformatics Multiple Alignment Editor"
 arch=(any)
 url="https://www.jalview.org/"
 license=('GPL3')
 depends=(java-runtime)
-
-####### Auto-generated using update_sources.sh
-### <INJECT_HERE> ###
-
-source=(
-  'https://www.jalview.org/webstart/jalview.jar'
-  'https://www.jalview.org/webstart/JGoogleAnalytics_0.3.jar'
-  'https://www.jalview.org/webstart/Jmol-14.6.4_2016.10.26.jar'
-  'https://www.jalview.org/webstart/VARNAv3-93.jar'
-  'https://www.jalview.org/webstart/VAqua5-patch.jar'
-  'https://www.jalview.org/webstart/activation.jar'
-  'https://www.jalview.org/webstart/apache-mime4j-0.6.jar'
-  'https://www.jalview.org/webstart/axis.jar'
-  'https://www.jalview.org/webstart/biojava-core-4.1.0.jar'
-  'https://www.jalview.org/webstart/biojava-ontology-4.1.0.jar'
-  'https://www.jalview.org/webstart/castor-1.1-cycle-xml.jar'
-  'https://www.jalview.org/webstart/commons-codec-1.3.jar'
-  'https://www.jalview.org/webstart/commons-discovery.jar'
-  'https://www.jalview.org/webstart/commons-logging-1.1.1.jar'
-  'https://www.jalview.org/webstart/groovy-all-2.4.12-indy.jar'
-  'https://www.jalview.org/webstart/htsjdk-1.133.jar'
-  'https://www.jalview.org/webstart/httpclient-4.0.3.jar'
-  'https://www.jalview.org/webstart/httpcore-4.0.1.jar'
-  'https://www.jalview.org/webstart/httpmime-4.0.3.jar'
-  'https://www.jalview.org/webstart/jabaws-min-client-2.2.0.jar'
-  'https://www.jalview.org/webstart/jalview_jnlp_vm.jar'
-  'https://www.jalview.org/webstart/java-json.jar'
-  'https://www.jalview.org/webstart/jaxrpc.jar'
-  'https://www.jalview.org/webstart/jdas-1.0.4.jar'
-  'https://www.jalview.org/webstart/jersey-client-1.19.jar'
-  'https://www.jalview.org/webstart/jersey-core-1.19.jar'
-  'https://www.jalview.org/webstart/jersey-json-1.19.jar'
-  'https://www.jalview.org/webstart/jetty-http-9.2.10.v20150310.jar'
-  'https://www.jalview.org/webstart/jetty-io-9.2.10.v20150310.jar'
-  'https://www.jalview.org/webstart/jetty-server-9.2.10.v20150310.jar'
-  'https://www.jalview.org/webstart/jetty-util-9.2.10.v20150310.jar'
-  'https://www.jalview.org/webstart/jfreesvg-2.1.jar'
-  'https://www.jalview.org/webstart/jhall.jar'
-  'https://www.jalview.org/webstart/json_simple-1.1.jar'
-  'https://www.jalview.org/webstart/jsoup-1.8.1.jar'
-  'https://www.jalview.org/webstart/jsr311-api-1.1.1.jar'
-  'https://www.jalview.org/webstart/jswingreader-0.3.jar'
-  'https://www.jalview.org/webstart/log4j-to-slf4j-2.0-rc2.jar'
-  'https://www.jalview.org/webstart/mail.jar'
-  'https://www.jalview.org/webstart/miglayout-4.0-swing.jar'
-  'https://www.jalview.org/webstart/regex.jar'
-  'https://www.jalview.org/webstart/saaj.jar'
-  'https://www.jalview.org/webstart/servlet-api-3.1.jar'
-  'https://www.jalview.org/webstart/slf4j-api-1.7.7.jar'
-  'https://www.jalview.org/webstart/slf4j-log4j12-1.7.7.jar'
-  'https://www.jalview.org/webstart/spring-core-3.0.5.RELEASE.jar'
-  'https://www.jalview.org/webstart/spring-web-3.0.5.RELEASE.jar'
-  'https://www.jalview.org/webstart/vamsas-client.jar'
-  'https://www.jalview.org/webstart/wsdl4j.jar'
-  'https://www.jalview.org/webstart/xercesImpl.jar'
-  'https://www.jalview.org/webstart/xml-apis.jar'
-  'logo.gif'
-  'jalview'
-  'jalview.desktop'
-)
-
-noextract=(
-  'jalview.jar'
-  'JGoogleAnalytics_0.3.jar'
-  'Jmol-14.6.4_2016.10.26.jar'
-  'VARNAv3-93.jar'
-  'VAqua5-patch.jar'
-  'activation.jar'
-  'apache-mime4j-0.6.jar'
-  'axis.jar'
-  'biojava-core-4.1.0.jar'
-  'biojava-ontology-4.1.0.jar'
-  'castor-1.1-cycle-xml.jar'
-  'commons-codec-1.3.jar'
-  'commons-discovery.jar'
-  'commons-logging-1.1.1.jar'
-  'groovy-all-2.4.12-indy.jar'
-  'htsjdk-1.133.jar'
-  'httpclient-4.0.3.jar'
-  'httpcore-4.0.1.jar'
-  'httpmime-4.0.3.jar'
-  'jabaws-min-client-2.2.0.jar'
-  'jalview_jnlp_vm.jar'
-  'java-json.jar'
-  'jaxrpc.jar'
-  'jdas-1.0.4.jar'
-  'jersey-client-1.19.jar'
-  'jersey-core-1.19.jar'
-  'jersey-json-1.19.jar'
-  'jetty-http-9.2.10.v20150310.jar'
-  'jetty-io-9.2.10.v20150310.jar'
-  'jetty-server-9.2.10.v20150310.jar'
-  'jetty-util-9.2.10.v20150310.jar'
-  'jfreesvg-2.1.jar'
-  'jhall.jar'
-  'json_simple-1.1.jar'
-  'jsoup-1.8.1.jar'
-  'jsr311-api-1.1.1.jar'
-  'jswingreader-0.3.jar'
-  'log4j-to-slf4j-2.0-rc2.jar'
-  'mail.jar'
-  'miglayout-4.0-swing.jar'
-  'regex.jar'
-  'saaj.jar'
-  'servlet-api-3.1.jar'
-  'slf4j-api-1.7.7.jar'
-  'slf4j-log4j12-1.7.7.jar'
-  'spring-core-3.0.5.RELEASE.jar'
-  'spring-web-3.0.5.RELEASE.jar'
-  'vamsas-client.jar'
-  'wsdl4j.jar'
-  'xercesImpl.jar'
-  'xml-apis.jar'
-)
-
-sha256sums=(
-  'c503c683d18750a08490ad9eec7e18877d752ae8ca7607c70e021cc4c0acf671'
-  '9e34f0f3b6fb78b07b20b354548ee2ae491e34a0b7dc387c303e20c6f1698fae'
-  'bf06e284c0412917482a440aa4ce5bfb64df1df3273a403c8193939f5b8d75db'
-  'd62831546d3d768ab3481846671eae9e0d8d9782096446db4f0cc46b2313fc68'
-  '05b0bf798a8ddd43e234c4120b77b1a65eb3f00e07791eebb518ef3e9f00fbbf'
-  '8559555902a4dcb07a1399a7f689116bd42e1a804b8f256aea44497d157b2369'
-  '718fd7958246f8e263807eddef4ea89dfd14e964c02c78a3f0ba0746bf032959'
-  'b51f38209abcece9e49bd369e70e1e3ba640f37842506030d090247153f01532'
-  'a8e308ed218978fc77aed03c0d504e4634014e46f0817575977c9523e3f188fc'
-  '1e4434bc5025dc73a084b278b53d5820dc61e471e88f48e31fec65eed430c910'
-  '54d1c95a880babc892e8da13768dd6e4a98d63e7f17c536f1e587400690103f7'
-  'd09d653869ce8d653cb96b865523b4ece48ec35d341f987d9b02a027507a3400'
-  '91e092f5a8cb744695f2e13247ec8672b4ba802129f414f93e2b98c494b3a4e5'
-  '4eb31efd61bded9537d06d06a7adcd720c344447e89f7046055c7bcdb36ca80d'
-  '3d922dc07e8f036a97315fcb746322814d222f81ada32b3ce7929cef6d228653'
-  '8206cb99aa57e4d797af1b165426be061383b4faf493b13b5e1ec9dfbb6b9d62'
-  '68f9c1664a027288adde4ef2f510079fd33fe02da4c0db4d5e3020039b11808d'
-  'b781df4e3041f0048c1fc71daf44b84420859b43468bb0499f0e5703a301a230'
-  '349e07ae02370b2b02408e7062b2af78f7755646a4693d25d5fd06fdccc6e211'
-  '610f598ec4ec89c3f7a07dbd72a93d0bb1814fee67c1ab8b006c06fcc342c78d'
-  'e02c7d7ebc66f9537349f76c69b65cd0f1d5676238b8b027f1f164514d1762c1'
-  '4a8fd2d40eae748fbfef7d8e8229271790e09a0cdcf1b9fab64ae83ee23847c8'
-  'd27dfecbb470ff51b8b1a27056f7e3d5224474c73ed9f4a00912636536e9e6d7'
-  '0ca32c5f5b343459c96b8bac245245c63057a632fa292ef94f9215cf572b516e'
-  '61fabcc3ace64986ecdbbc30762951049642d5d43ba7031a9fa684818edd4dd7'
-  'fad5dc8b11c5066183720a65d649f4f216e46b9e46bbc7f6454d16342b605c3e'
-  'd7a26238d61e872bb78f77d92f2c79eb1d2db49b94fa41fe13093c6fe83632ba'
-  'd6a0c276eaa44f7b1b20f6bd3d48359d5628ab6a525c7a948f374d1de8d7be1f'
-  'f18875517fd04179b3fc94ee0001635d8323dcfab86f0646d9847d76a63b701f'
-  'f29503a43ff3de272226036334764cd2f0e4714f7eaefa5807c89bd9a43b558b'
-  'e858dae934f5cf01f473a369040de9eb016274ac7e03518768c8eb0fb03985f8'
-  'f8022bb59e92032acf7f0b2edb916d2c000f017786cda500d94f5671c01af562'
-  'd9b7a3febcff52ab0e328a79ec60bacd3875ab451cf0400bb02a4cf9d72e9362'
-  '1fc89d9247779496fdbf32c75e591146ed9a2f180241531e82938267238d495c'
-  '5377f928f2c8f30302914a86cd4e357b7a46455027319fd2663dc418a0d8df5e'
-  '9b47ad4fb5f24172919a50d2883c99275f185d8a912c498146e1b6d5f00c2540'
-  'c750df074a6198be47f8c37f5fb7a795d3ee48bb2a9ebd5d50ca114aede3b3d7'
-  '4b458f7cb9b01b78a747241bfb1150353c73ad9899fd4e6b215b1996308838e2'
-  'ab1b9523efcba2993198911e0bd64f35a80c5ec1c443ea9fb62e33940512a45b'
-  '742be53a8b87095bd5b8e42635058db567bbf3e081ef91a40fb4ef09746ae452'
-  '87d54d16a26b2b0163a7cf18557c0f208c928b5309654389f5e098147982f6b4'
-  '170d6e60f775f399e7b74adb759c4393ff8f40e57fee6bb2e55410f8057eec65'
-  '4f1729ffee579454e2ccd339b7c14c5f6f4d52cacd04394112b8f5d1a5815287'
-  '1246368d10316a01a58c9cb062cd779dbdfe2e69b9f3e09a4d4d8ca3580ac0d9'
-  'aaf1c73b28bed5f5d7b4549a590dec7419d621945c3b3f21011e6bf93211e12c'
-  'd54fc5f333bd6ac11377281232512fd8e65b32549271ea7a92d5a28f50b23cdf'
-  'c9d303ed6f8c478d991dc2096eaeb548ab76e4d532cc2160fe4dfc78cdc37b1a'
-  'bd0f7da4017b5f381e71e7c1c072d8060a5469c769a682ead662fc189f5f808f'
-  'ade0c607d1d6313d2381523ce965391369736ba5d80c0603a7bde3df08d30bb6'
-  'e3f0bb4626475674428ab64c864ec48b43d01620aebcdcc3e58ac248d0acde8e'
-  '49c785261ee701eec7c6b7d4b2839077d52b2b668de0a4298f0848d89ef5cd0d'
-  '362790ef6d3e3c537a6d31663a0e7f3ec9664c90cb9dc6df4a80b016f474eaa4'
-  'd5d4f97f520d58ddb8f2552800f946c2ab6c89c3dd105b7a9cd777b9925bc17e'
-  '4c87a84ec39e677fe2922a5e78cf68cf508ec8dff5211193b11aac7cb1cf4211'
-)
-
-### </INJECT_HERE> ###
+source=("http://www.jalview.org/getdown/release/install4j/1.8/jalview-2_11_1_4-unix-java_8.tar.gz"
+    'jalview'
+    'jalview.desktop')
+noextract=("jalview-2_11_1_4-unix-java_8.tar.gz")
+sha256sums=('32fa6106f3afedf7e60d4b1c8006846903e4cdaa0730190cfea399ab49202c05'
+    'dbe5edfa9b17a1f85083b5aae16ef7a186a0d0035e6a81761cf73d0e1121ce58'
+    'd9e0823d3b724d1c373763864d5daf6ebd59d1511347ec461310324afa45448e')
+
+prepare() {
+    mkdir -p ./$pkgname-$pkgver
+    tar -xzvf *.tar.gz -C ./$pkgname-$pkgver --strip-components 1
+}
 
 package() {
-  cd "$srcdir/"
+    install -Dm755 -t "${pkgdir}/usr/bin/" ${pkgname}
+    install -Dm644 -t $pkgdir/usr/share/applications/ jalview.desktop
 
-  # set up directory structure
-  mkdir -p $pkgdir/usr/{share/{applications,pixmaps,java/$pkgname},bin}
+    install -Dm644 -t "$pkgdir/usr/share/java/$pkgname" $srcdir/$pkgname-$pkgver/release/*.jar
 
-  install -Dm644 *.jar $pkgdir/usr/share/java/$pkgname/
-  install -Dm755 jalview $pkgdir/usr/bin/
-  install -Dm644 logo.gif $pkgdir/usr/share/pixmaps/jalview.gif
-  install -Dm644 jalview.desktop $pkgdir/usr/share/applications/
+    install -Dm644 $srcdir/$pkgname-$pkgver/resource/JalviewLogo_Huge.png $pkgdir/usr/share/pixmaps/jalview_logo.png
+    install -Dm644 $srcdir/$pkgname-$pkgver/resource/jalview_logos.ico $pkgdir/usr/share/pixmaps/jalview_logos.ico
 }
-
-# vim:set ts=2 sw=2 et:
diff --git a/jalview b/jalview
index c1c64c839c08..dab8b9d022b0 100755
--- a/jalview
+++ b/jalview
@@ -5,8 +5,7 @@ mainclass="jalview.bin.Jalview"
 basedir="/usr/share/java/$progname"
 
 # build classpath: all jars in $basedir
-cp=$( ls $basedir/*.jar | xargs echo | sed "s/ /:/g" );
-
+cp=$(ls $basedir/*.jar | xargs echo | sed "s/ /:/g")
 
 # run jar
-"$JAVA_HOME/bin/java" -cp $cp $mainclass
+"/usr/bin/java" -cp $cp $mainclass
diff --git a/jalview.desktop b/jalview.desktop
index af5ccfb89830..2b52f868fcb4 100644
--- a/jalview.desktop
+++ b/jalview.desktop
@@ -2,7 +2,7 @@
 Name=Jalview
 Comment=A multiple alignment editor
 Exec=jalview
-Icon=/usr/share/pixmaps/jalview.gif
+Icon=/usr/share/pixmaps/jalview_logos.ico
 StartupNotify=true
 Type=Application
 Categories=Education;Science;Bioinformatics;