tempest, pibuss: merge into beast

This commit is contained in:
Kuoi 2023-04-29 00:04:17 +08:00
parent 68cff5a479
commit 93554af37c
18 changed files with 161 additions and 340 deletions

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@ -1,68 +1,186 @@
# Maintainer: Malacology <guoyizhang at malacology dot net>
# Contributor: Malacology <guoyizhang at malacology dot net>
pkgname=beast
pkgver=sars__cov__2__origins
pkgrel=2
pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
basename=beast
pkgname=('beast' 'beastgen' 'pibuss' 'coalgen' 'phylogeography' 'tempest' )
pkgver=1.10.4
pkgrel=0
arch=('x86_64')
url="http://beast.community/"
license=('LGPL')
source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/${pkgver//__/-}.tar.gz"
"beast.desktop"
"beast-beauti.desktop"
"beast-loganalyser.desktop"
"beast-logcombiner.desktop"
"beast-treeannotator.desktop"
"beast-treestat.desktop"
"fix_bin.patch")
sha256sums=('fab8750313b66844f4dd8dcacfa55913f30bb877bded87057ba347d38cc9dc75'
'fa9841f5005be6d743ad278b037de0eb329c642de62e4996cc1df31272ffa185'
'e3897ee92348b3e48010af739fcbf7fbb38bcc2c18e1ceb30cd147b3c7067b2d'
'dcf674ebe5f1b7b13e746441f7a28a9b0fa86c03f3bef27833c532f323cb6644'
'75842d174f246c38dc4600357ef8b41f67e5f12cbd7dba779d224f99b531cb1d'
'6e63a619a6fb3101606a85dbc352d579e343d167cf79be67ccf31ed1544d5fd2'
'3a21774077658117f36bd289901ec1d560a66bbe435ba4ddbc1980c558fa7362'
'086b899c6f4bfa43d4af61d497c0265d087e919de5723faa6b3e58ae48fb6813')
source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/v${pkgver//__/-}.tar.gz"
"$basename.patch::https://patch-diff.githubusercontent.com/raw/beast-dev/beast-mcmc/pull/1149.patch")
sha256sums=('6e28e2df680364867e088acd181877a5d6a1d664f70abc6eccc2ce3a34f3c54a'
'2f65ebb8c45feed0b2969276c7caae147b83f4f1dd4fc5e1d705aada2c4163e1')
depends=('java-runtime=8')
makedepends=('java-environment=8' 'ant' 'cmake' 'beagle-lib')
optdepends=('beagle-lib')
build() {
cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
ant dist
java -jar -Djava.library.path=/usr/lib build/dist/beast.jar -beagle_info
makedepends=('java-environment=8' 'ant' 'cmake' 'beagle-lib' 'gendesk')
prepare(){
cd $srcdir/$basename-mcmc-${pkgver//__/-}
patch -p1 < $srcdir/$basename.patch
}
package() {
#install desktop
cd $srcdir/
for des in $(ls *.desktop)
do
install -Dm 755 $des $pkgdir/usr/share/applications/$des
done
build() {
cd $srcdir/$basename-mcmc-${pkgver//__/-}
ant linux
java -jar -Djava.library.path=/usr/lib build/dist/beast.jar -beagle_info
cp -r build/dist dist_beast
ant -buildfile build_beastgen.xml package
cp -r dist dist_beastgen
ant -buildfile build_bss.xml linux
cp -r dist dist_pibuss
ant -buildfile build_coalsim.xml dist
cp -r dist dist_coalgen
ant -buildfile build_phylogeography.xml package
cp -r dist dist_phylogeography
ant -buildfile build_tempest.xml dist
cp -r dist dist_tempest
}
package_beast() {
pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
cd build/dist
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_beast
for jar in $(ls *.jar)
do
install -Dm 755 $jar $pkgdir/usr/share/$pkgname/$jar
done
# install bin
cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
# install bin, desktop
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release/Linux/scripts
patch -N -i $srcdir/fix_bin.patch
sed -i "s@/usr/local/lib@/usr/lib@g" *
sed -i "s@\$BEAST/lib@/usr/share/beast@g" *
for bin in $(ls)
do
install -Dm 755 $bin $pkgdir/usr/bin/$bin
install -Dm 755 $bin $pkgdir/usr/bin/$pkgname-$bin
gendesk --pkgname "$bin" --pkgdesc "$pkgdesc" --exec="$pkgname-$bin" --icon="/usr/share/pixmaps/$bin.png"
install -Dm 755 $bin.desktop $pkgdir/usr/share/applications/$basename-$bin.desktop
done
# install icons
cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release/common/icons
for icon in $(ls *.png)
do
install -Dm 644 $icon $pkgdir/usr/share/pixmaps/$icon
install -Dm 644 $icon $pkgdir/usr/share/pixmaps/${icon,,}
done
# ln icons
for png in loganalyser logcombiner treeannotator
do
ln -s /usr/share/pixmaps/utility.png $pkgdir/usr/share/pixmaps/$png.png
done
}
package_beastgen(){
pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_beastgen
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_beastgen/common/bin/
sed -i "s@\$BEASTGEN/lib@/usr/share/beastgen@g" beastgen
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
}
package_pibuss(){
pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_pibuss
install -Dm 755 buss.jar $pkgdir/usr/share/$pkgname/buss.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_pibuss/Linux/scripts/
sed -i "s@/usr/local/lib@/usr/lib@g" pibuss
sed -i "s@\$PIBUSS/lib@/usr/share/pibuss@g" pibuss
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
# install icons
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_pibuss/Linux/icons
install -Dm 644 $pkgname.png $pkgdir/usr/share/pixmaps/$pkgname.png
# install pibuss.desktop
gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
}
package_coalgen(){
pkgdesc="BEAST Coalescent Tree Simulator https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_coalgen
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
echo "COALGEN_LIB=/usr/share/coalgen" >> $pkgname
echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$COALGEN_LIB:/usr/lib\" -jar \$COALGEN_LIB/coalgen.jar \$*" >> $pkgname
chmod +x $pkgname
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
# icon
cd $srcdir/$basename-mcmc-${pkgver//__/-}
install -Dm 644 src/dr/app/coalgen/images/CoalGen.png $pkgdir/usr/share/pixmaps/$pkgname.png
# desktop
gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
}
package_phylogeography(){
pkgdesc="BEAST PhyloGeography https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_$pkgname
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_phylogeography/common/bin/
for bin in continuous_tree_to_kml discrete_rate_prior_generator discrete_tree_to_kml rate_indicator_bf timeslicer
do
sed -i "s@\$PHYLOGEOGRAPHY/lib@/usr/share/phylogeography@g" $bin
install -Dm 755 $bin $pkgdir/usr/bin/$bin
done
}
package_tempest(){
pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007"
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_$pkgname
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
echo "TEMPEST_LIB=/usr/share/tempest" >> $pkgname
echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$TEMPEST_LIB:/usr/lib\" -jar \$TEMPEST_LIB/tempest.jar \$*" >> $pkgname
chmod +x $pkgname
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
# install ico
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_$pkgname/Windows/icons
install -Dm 644 TempEst.ico $pkgdir/usr/share/pixmaps/$pkgname.ico
# desktop
gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.ico"
install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
}

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@ -1,16 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=beauti %U
Icon=beauti
MimeType=
Name=beauti
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root
X-GNOME-UsesNotifications=true

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@ -1,16 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=loganalyser %U
Icon=utility
MimeType=
Name=loganalyser
Name[zh]=loganalyser
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,16 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=logcombiner %U
Icon=utility
MimeType=
Name=logcombiner
Name[zh]=logcombiner
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,17 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=treeannotator %U
GenericName=
GenericName[zh]=
Icon=utility
MimeType=
Name=treeannotator
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,16 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=treestat %U
Icon=TreeStat
MimeType=
Name=treestat
Name[zh]=treestat
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,18 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=beast %U
GenericName=
GenericName[zh]=
Icon=beast
MimeType=
Name=beast
Name[zh]=beast
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,72 +0,0 @@
diff --git a/beast b/beast
index 2607b4d..6d50a5f 100755
--- a/beast
+++ b/beast
@@ -22,5 +22,5 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
-java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/local/lib:$LD_LIBRARY_PATH" -cp "$BEAST_LIB/beast.jar" dr.app.beast.BeastMain $*
+BEAST_LIB="/usr/share/beast"
+java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/lib:$LD_LIBRARY_PATH" -cp "$BEAST_LIB/beast.jar" dr.app.beast.BeastMain $*
diff --git a/beauti b/beauti
index d2cb818..bc57736 100755
--- a/beauti
+++ b/beauti
@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
+BEAST_LIB="/usr/share/beast"
java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
diff --git a/loganalyser b/loganalyser
index a728320..beaee3c 100755
--- a/loganalyser
+++ b/loganalyser
@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
+BEAST_LIB="/usr/share/beast"
java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
diff --git a/logcombiner b/logcombiner
index 5fe9821..4fb5653 100755
--- a/logcombiner
+++ b/logcombiner
@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
+BEAST_LIB="/usr/share/beast"
java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
diff --git a/treeannotator b/treeannotator
index c4eafc2..b9d065d 100755
--- a/treeannotator
+++ b/treeannotator
@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
+BEAST_LIB="/usr/share/beast"
java -Xms64m -Xmx4096m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
diff --git a/treestat b/treestat
index d35bf6c..b584175 100755
--- a/treestat
+++ b/treestat
@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
cd "$saveddir"
fi
-BEAST_LIB="$BEAST/lib"
+BEAST_LIB="/usr/share/beast"
java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*

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@ -7,12 +7,10 @@ pre_build_script: |
run_cmd(['updpkgsums'])
post_build_script: |
git_pkgbuild_commit()
update_aur_repo()
update_on:
- source: github
github: beast-dev/beast-mcmc
use_latest_release: true
# prefix: 'v'
# include_regex: '[^v]+'
prefix: 'v'
repo_depends:
- beagle-lib

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@ -1,25 +0,0 @@
# Maintainer: Malacology <guoyizhang at malacology dot net>
# Contributor: Malacology <guoyizhang at malacology dot net>
pkgname=pibuss
pkgver=1.4
_pkgver=${pkgver//./-}
pkgrel=5
depends=(
'java-runtime'
)
pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133"
arch=('x86_64')
url="https://rega.kuleuven.be/cev/ecv/software/pibuss"
license=('custom')
source=("https://rega.kuleuven.be/cev/ecv/software/pibuss_files/pibuss-v${_pkgver}.jar" "pibuss.desktop" "pibuss.png")
sha256sums=('a9d397ec6815339a2d4b268b99897a7d42250d4cd649b1ad2e458033e48b432c'
'96cc7d7b0ffce5358b14c981ac84355237f5c9c5599ca9ead16f1d1f11d29f40'
'18a508a9fc4fb169d366b7158095aa001f3ccc389f6aca8f2ae2df0b84413003')
package() {
install -dm755 "$pkgdir"/usr/share/{applications,pibuss}
install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
install -m 755 ${srcdir}/*.png ${pkgdir}/usr/share/pibuss
install -m 755 ${srcdir}/pibuss-v${_pkgver}.jar ${pkgdir}/usr/share/pibuss/pibuss.jar
}

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@ -1,11 +0,0 @@
#!/usr/bin/env python3
from lilaclib import *
def pre_build():
update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
run_cmd(['updpkgsums'])
def post_build():
git_add_files('PKGBUILD')
git_commit()
update_aur_repo()

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@ -1,8 +0,0 @@
build_prefix: extra-x86_64
maintainers:
- github: starsareintherose
email: kuoi@bioarchlinux.org
update_on:
- source: regex
url: https://rega.kuleuven.be/cev/ecv/software/pibuss
regex: pibuss_v(\d+.\d+).jar

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@ -1,19 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=java -jar /usr/share/pibuss/pibuss.jar
GenericName=
GenericName[zh]=
Icon=/usr/share/pibuss/pibuss.png
MimeType=
Name=ΠBUSS
Name[zh]=ΠBUSS
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root

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@ -1,25 +0,0 @@
# Maintainer: Malacology <guoyizhang at malacology dot net>
# Contributor: Malacology <guoyizhang at malacology dot net>
pkgname=tempest
pkgver=1.5.3
pkgrel=5
depends=(
'java-runtime'
)
pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007"
arch=('x86_64')
url="http://tree.bio.ed.ac.uk/software/tempest/"
license=('GPL2')
source=("https://raw.githubusercontent.com/beast-dev/Tempest/main/release/TempEst_v${pkgver}.tgz" "tempest.desktop")
sha256sums=('83e482a7ba946e38606cc3331765db45b4331337d92d030ebeb537e3e16fa44e'
'2af28c04f9d96f046947efeab28c27552be88ac56af0d8f1a0db2e439a228c45')
package() {
install -dm755 "$pkgdir"/usr/{bin,share/{applications,tempest}}
install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
mv ${srcdir}/TempEst_v${pkgver}/* ${pkgdir}/usr/share/tempest
chmod +x ${pkgdir}/usr/share/tempest/bin/tempest
ln -s /usr/share/tempest/bin/tempest ${pkgdir}/usr/bin/tempest
}

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@ -1,10 +0,0 @@
#!/usr/bin/env python3
from lilaclib import *
def pre_build():
update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
run_cmd(['updpkgsums'])
def post_build():
git_add_files('PKGBUILD')
git_commit()

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@ -1,8 +0,0 @@
build_prefix: extra-x86_64
maintainers:
- github: starsareintherose
email: kuoi@bioarchlinux.org
update_on:
- source: regex
url: https://github.com/beast-dev/Tempest/tree/main/release
regex: TempEst_v(\d+.\d+.\d+).tgz

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@ -1,18 +0,0 @@
[Desktop Entry]
Categories=
Encoding=UTF-8
Exec=java -jar /usr/share/tempest/lib/tempest.jar
GenericName=
GenericName[zh]=
Icon=/usr/share/tempest/images/tempest.png
MimeType=
Name=TempEst
ServiceTypes=
SwallowExec=
SwallowTitle=
Terminal=false
TerminalOptions=
Type=Application
X-KDE-SubstituteUID=false
X-KDE-Username=root