mirror of
https://github.com/BioArchLinux/Packages.git
synced 2025-03-10 12:02:42 +00:00
artemis: build from source prepare
This commit is contained in:
Kuoi
parent
d133fe9751
commit
1850076697
8 changed files with 522 additions and 0 deletions
75
prepare/artemis/PKGBUILD
Normal file
75
prepare/artemis/PKGBUILD
Normal file
|
|
@ -0,0 +1,75 @@
|
|||
# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
|
||||
# Contributor: Clint Valentine <valentine.clint@gmail.com>
|
||||
|
||||
pkgname=artemis
|
||||
_pkgname=Artemis
|
||||
pkgver=18.2.0
|
||||
pkgrel=5
|
||||
pkgdesc='A genome viewer and annotation tool that visualizes biological sequence features'
|
||||
arch=('x86_64')
|
||||
url=https://www.sanger.ac.uk/science/tools/"${pkgname}"
|
||||
license=('GPL2')
|
||||
depends=('java-runtime')
|
||||
makedepends=('java-environment' 'maven')
|
||||
source=($pkgname-$pkgver.tar.gz::https://github.com/sanger-pathogens/Artemis/archive/refs/tags/v${pkgver}.tar.gz
|
||||
act.desktop
|
||||
artemis.desktop
|
||||
bamview.desktop
|
||||
dnaplotter.desktop)
|
||||
sha256sums=('842c055f5cce021adbaea4f076b2ea80335ab1e44fbaa34b2ab608df6314a18e'
|
||||
'a7dda77f6518c98af6df88ba5d725f1b89d86aca125240f63a9c6e08afeb2a24'
|
||||
'dea9a1cc47b110c4f6ebe17c1b698866082997ffd9e6008d89847ddf745a0789'
|
||||
'3ca519b00ffac02d635a62884996ad5b8c4580d8ffe8fcd427ee4edee1562f00'
|
||||
'ef584b45f9c92da15511779f20a1a1449915315066662e4c142ea4cd92dd717c')
|
||||
#prepare() {
|
||||
#scripts=('act' 'art' 'bamview' 'dnaplotter')
|
||||
# cd $srcdir/$_pkgname-$pkgver
|
||||
# patch -N -i $srcdir/fix_bin.patch
|
||||
#}
|
||||
build() {
|
||||
cd $srcdir/$_pkgname-$pkgver
|
||||
mvn validate
|
||||
mvn package
|
||||
}
|
||||
package() {
|
||||
bina=('act' 'art' 'bamview' 'dnaplotter')
|
||||
scripts=('act' 'artemis' 'bamview' 'dnaplotter')
|
||||
|
||||
# desktop
|
||||
cd $srcdir/
|
||||
for des in ${scripts[@]}
|
||||
do
|
||||
install -Dm 755 $des.desktop $pkgdir/usr/share/applications/$des.desktop
|
||||
done
|
||||
|
||||
# bin
|
||||
cd $srcdir/$_pkgname-$pkgver
|
||||
for bin in ${bina[@]}
|
||||
do
|
||||
install -Dm 775 $bin $pkgdir/usr/share/$pkgname/$bin
|
||||
done
|
||||
|
||||
# jar
|
||||
cd $srcdir/$_pkgname-$pkgver/target/jars
|
||||
for jar in $(ls *.jar)
|
||||
do
|
||||
install -Dm 755 $jar $pkgdir/usr/share/$pkgname/target/jars/$jar
|
||||
done
|
||||
|
||||
# icons
|
||||
cd $srcdir/$_pkgname-$pkgver/target/classes/images
|
||||
for icn in ${scripts[@]}
|
||||
do
|
||||
mv ${icn}_icon.png ${icn}.png
|
||||
install -Dm 644 ${icn}.png $pkgdir/usr/share/pixmaps/${icn}.png
|
||||
done
|
||||
|
||||
# link bin
|
||||
cd $srcdir/$_pkgname-$pkgver
|
||||
mkdir -p $pkgdir/usr/bin
|
||||
for bin in ${bina[@]}
|
||||
do
|
||||
ln -s /usr/share/$pkgname/$bin $pkgdir/usr/bin/$bin
|
||||
done
|
||||
|
||||
}
|
||||
16
prepare/artemis/act.desktop
Executable file
16
prepare/artemis/act.desktop
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
[Desktop Entry]
|
||||
Categories=
|
||||
Encoding=UTF-8
|
||||
Exec=act
|
||||
GenericName=
|
||||
Icon=act
|
||||
MimeType=
|
||||
Name=act
|
||||
ServiceTypes=
|
||||
SwallowExec=
|
||||
SwallowTitle=
|
||||
Terminal=false
|
||||
TerminalOptions=
|
||||
Type=Application
|
||||
X-KDE-SubstituteUID=false
|
||||
X-KDE-Username=root
|
||||
16
prepare/artemis/artemis.desktop
Executable file
16
prepare/artemis/artemis.desktop
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
[Desktop Entry]
|
||||
Categories=
|
||||
Encoding=UTF-8
|
||||
Exec=art
|
||||
GenericName=
|
||||
Icon=artemis
|
||||
MimeType=
|
||||
Name=artemis
|
||||
ServiceTypes=
|
||||
SwallowExec=
|
||||
SwallowTitle=
|
||||
Terminal=false
|
||||
TerminalOptions=
|
||||
Type=Application
|
||||
X-KDE-SubstituteUID=false
|
||||
X-KDE-Username=root
|
||||
16
prepare/artemis/bamview.desktop
Executable file
16
prepare/artemis/bamview.desktop
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
[Desktop Entry]
|
||||
Categories=
|
||||
Encoding=UTF-8
|
||||
Exec=bamview
|
||||
GenericName=
|
||||
Icon=bamview
|
||||
MimeType=
|
||||
Name=bamview
|
||||
ServiceTypes=
|
||||
SwallowExec=
|
||||
SwallowTitle=
|
||||
Terminal=false
|
||||
TerminalOptions=
|
||||
Type=Application
|
||||
X-KDE-SubstituteUID=false
|
||||
X-KDE-Username=root
|
||||
16
prepare/artemis/dnaplotter.desktop
Executable file
16
prepare/artemis/dnaplotter.desktop
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
[Desktop Entry]
|
||||
Categories=
|
||||
Encoding=UTF-8
|
||||
Exec=dnaplotter
|
||||
GenericName=
|
||||
Icon=dnaplotter
|
||||
MimeType=
|
||||
Name=dnaplotter
|
||||
ServiceTypes=
|
||||
SwallowExec=
|
||||
SwallowTitle=
|
||||
Terminal=false
|
||||
TerminalOptions=
|
||||
Type=Application
|
||||
X-KDE-SubstituteUID=false
|
||||
X-KDE-Username=root
|
||||
362
prepare/artemis/fix_bin.patch
Normal file
362
prepare/artemis/fix_bin.patch
Normal file
|
|
@ -0,0 +1,362 @@
|
|||
Description: Simplifying the provided launchers
|
||||
Many options or tricks are useless on a Debian system.
|
||||
The paths are also adapted to the Debian install.
|
||||
Author: Pierre Gruet <pgt@debian.org>
|
||||
Forwarded: not-needed
|
||||
Last-Update: 2020-09-06
|
||||
|
||||
--- a/act
|
||||
+++ b/act
|
||||
@@ -38,36 +38,6 @@
|
||||
exit 0
|
||||
}
|
||||
|
||||
-add_proxy_properties() {
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_PROXY
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_proxy
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" != "" ]]
|
||||
- then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
|
||||
- fi
|
||||
-}
|
||||
-
|
||||
-#
|
||||
-# Resolve script path (inc symlinks)
|
||||
-#
|
||||
-SOURCE="${BASH_SOURCE[0]}"
|
||||
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||
- SOURCE="$(readlink "$SOURCE")"
|
||||
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
-done
|
||||
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||
-
|
||||
-
|
||||
# Special Sanger override on chado PGUSER
|
||||
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
|
||||
then
|
||||
@@ -93,28 +63,6 @@
|
||||
shift
|
||||
done
|
||||
|
||||
-
|
||||
-JAR_NAME=act.jar
|
||||
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||
-
|
||||
-#
|
||||
-# Use a custom Java version if necessary
|
||||
-#
|
||||
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||
-then
|
||||
- JAVA=`which java`
|
||||
-else
|
||||
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||
-fi
|
||||
-
|
||||
-#
|
||||
-# Allow URLs to work from behind firewalls.
|
||||
-#
|
||||
-add_proxy_properties
|
||||
-
|
||||
#
|
||||
# "-mx2g" sets the maximum amount of memory to use.
|
||||
# This may need to be increased when dealing with large files
|
||||
@@ -132,20 +80,12 @@
|
||||
#
|
||||
FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
|
||||
|
||||
-PLATTMP=`uname`
|
||||
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||
-then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=ACT"
|
||||
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||
-fi
|
||||
-
|
||||
if [[ "$QUIET" = no ]]
|
||||
then
|
||||
echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
|
||||
fi
|
||||
|
||||
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*
|
||||
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/act.jar $*
|
||||
result=$?
|
||||
|
||||
exit $result
|
||||
--- a/art
|
||||
+++ b/art
|
||||
@@ -44,36 +44,6 @@
|
||||
exit 0
|
||||
}
|
||||
|
||||
-add_proxy_properties() {
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_PROXY
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_proxy
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" != "" ]]
|
||||
- then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
|
||||
- fi
|
||||
-}
|
||||
-
|
||||
-#
|
||||
-# Resolve script path (inc symlinks)
|
||||
-#
|
||||
-SOURCE="${BASH_SOURCE[0]}"
|
||||
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||
- SOURCE="$(readlink "$SOURCE")"
|
||||
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
-done
|
||||
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||
-
|
||||
-
|
||||
# Special Sanger override on chado PGUSER
|
||||
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
|
||||
then
|
||||
@@ -99,28 +69,6 @@
|
||||
shift
|
||||
done
|
||||
|
||||
-
|
||||
-JAR_NAME=artemis.jar
|
||||
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||
-
|
||||
-#
|
||||
-# Use a custom Java version if necessary
|
||||
-#
|
||||
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||
-then
|
||||
- JAVA=`which java`
|
||||
-else
|
||||
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||
-fi
|
||||
-
|
||||
-#
|
||||
-# Allow URLs to work from behind firewalls.
|
||||
-#
|
||||
-add_proxy_properties
|
||||
-
|
||||
#
|
||||
# "-mx2g" sets the maximum amount of memory to use.
|
||||
# This may need to be increased when dealing with large files
|
||||
@@ -139,20 +87,12 @@
|
||||
#
|
||||
FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
|
||||
|
||||
-PLATTMP=`uname`
|
||||
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||
-then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis"
|
||||
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||
-fi
|
||||
-
|
||||
if [[ "$QUIET" = "no" ]]
|
||||
then
|
||||
echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
|
||||
fi
|
||||
|
||||
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*
|
||||
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/artemis.jar $*
|
||||
result=$?
|
||||
|
||||
exit $result
|
||||
--- a/bamview
|
||||
+++ b/bamview
|
||||
@@ -6,57 +6,7 @@
|
||||
|
||||
QUIET=no
|
||||
|
||||
-add_proxy_properties() {
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_PROXY
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_proxy
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" != "" ]]
|
||||
- then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
|
||||
- fi
|
||||
-}
|
||||
-
|
||||
-#
|
||||
-# Resolve script path (inc symlinks)
|
||||
-#
|
||||
-SOURCE="${BASH_SOURCE[0]}"
|
||||
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||
- SOURCE="$(readlink "$SOURCE")"
|
||||
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
-done
|
||||
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||
-
|
||||
-
|
||||
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
|
||||
-JAR_NAME=bamview.jar
|
||||
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||
-
|
||||
-#
|
||||
-# Use a custom Java version if necessary
|
||||
-#
|
||||
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||
-then
|
||||
- JAVA=`which java`
|
||||
-else
|
||||
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||
-fi
|
||||
-
|
||||
-#
|
||||
-# Allow URLs to work from behind firewalls.
|
||||
-#
|
||||
-add_proxy_properties
|
||||
|
||||
#
|
||||
# "-mx2g" sets the maximum amount of memory to use.
|
||||
@@ -69,20 +19,12 @@
|
||||
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
|
||||
fi
|
||||
|
||||
-PLATTMP=`uname`
|
||||
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||
-then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
|
||||
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||
-fi
|
||||
-
|
||||
if [[ "$QUIET" = "no" ]]
|
||||
then
|
||||
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
|
||||
fi
|
||||
|
||||
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
|
||||
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/bamview.jar $*
|
||||
result=$?
|
||||
|
||||
exit $result
|
||||
--- a/dnaplotter
|
||||
+++ b/dnaplotter
|
||||
@@ -25,37 +25,6 @@
|
||||
exit 0
|
||||
}
|
||||
|
||||
-add_proxy_properties() {
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_PROXY
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" = "" ]]
|
||||
- then
|
||||
- http_proxy=$HTTP_proxy
|
||||
- fi
|
||||
-
|
||||
- if [[ "$http_proxy" != "" ]]
|
||||
- then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
|
||||
- fi
|
||||
-}
|
||||
-
|
||||
-
|
||||
-#
|
||||
-# Resolve script path (inc symlinks)
|
||||
-#
|
||||
-SOURCE="${BASH_SOURCE[0]}"
|
||||
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||
- SOURCE="$(readlink "$SOURCE")"
|
||||
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
-done
|
||||
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||
-
|
||||
-
|
||||
#
|
||||
# Parse arguments.
|
||||
#
|
||||
@@ -75,28 +44,6 @@
|
||||
shift
|
||||
done
|
||||
|
||||
-
|
||||
-JAR_NAME=dnaplotter.jar
|
||||
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||
-
|
||||
-#
|
||||
-# Use a custom Java version if necessary
|
||||
-#
|
||||
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||
-then
|
||||
- JAVA=`which java`
|
||||
-else
|
||||
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||
-fi
|
||||
-
|
||||
-#
|
||||
-# Allow URLs to work from behind firewalls.
|
||||
-#
|
||||
-add_proxy_properties
|
||||
-
|
||||
#
|
||||
# "-mx2g" sets the maximum amount of memory to use.
|
||||
# This may need to be increased when dealing with large files
|
||||
@@ -108,20 +55,12 @@
|
||||
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
|
||||
fi
|
||||
|
||||
-PLATTMP=`uname`
|
||||
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||
-then
|
||||
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"
|
||||
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||
-fi
|
||||
-
|
||||
if [[ "$QUIET" = "no" ]]
|
||||
then
|
||||
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
|
||||
fi
|
||||
|
||||
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
|
||||
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/dnaplotter.jar $TEMPLATE_FILE_ARG
|
||||
result=$?
|
||||
|
||||
exit $result
|
||||
|
||||
|
||||
16
prepare/artemis/lilac.yaml
Normal file
16
prepare/artemis/lilac.yaml
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
build_prefix: extra-x86_64
|
||||
maintainers:
|
||||
- github: starsareintherose
|
||||
email: kuoi@bioarchlinux.org
|
||||
pre_build_script: |
|
||||
update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
|
||||
run_cmd(['updpkgsums'])
|
||||
post_build_script: |
|
||||
git_add_files('PKGBUILD')
|
||||
git_commit()
|
||||
update_aur_repo()
|
||||
update_on:
|
||||
- source: github
|
||||
github: sanger-pathogens/Artemis
|
||||
use_max_tag: true
|
||||
prefix: 'v'
|
||||
5
prepare/artemis/readme
Normal file
5
prepare/artemis/readme
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
# Artemis
|
||||
|
||||
art and act shell script doesn't work.
|
||||
|
||||
Fix it and then this package can work
|
||||
Loading…
Add table
Reference in a new issue