Added version 2.7.6

2.7.6/Singularity

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+Bootstrap: docker
+From: ubuntu:20.04
+
+%labels
+    AUTHOR icaoberg
+    EMAIL [email protected]
+    SUPPORT [email protected]
+    REPOSITORY http://gitub.com/pscedu/singularity-beast2
+    COPYRIGHT Copyright © 2024 Pittsburgh Supercomputing Center. All Rights Reserved.
+    VERSION 2.7.6
+
+%files
+    BEAST.v2.7.6.Linux.x86.tgz /opt/    
+
+%environment
+    export PATH=$PATH:/opt/beast/bin
+
+%post
+    apt update
+    apt install -y default-jdk
+    apt install -y libxext6 libxrender1 libxtst6 libxi6
+    cd /opt
+    tar -xvf BEAST.v2.7.6.Linux.x86.tgz && rm -fv BEAST.v2.7.6.Linux.x86.tgz
+
+%runscript
+    /opt/beast/bin/applauncher

2.7.6/applauncher

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=applauncher
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/beast

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=beast
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/beauti

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=beauti
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/build.sh

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+#!/bin/bash
+
+IMAGE=singularity-BEAST2-2.7.6.sif
+DEFINITION=Singularity
+
+if [ -f $IMAGE ]; then
+	rm -fv $IMAGE
+fi
+
+sudo singularity build $IMAGE $DEFINITION
+
+if [ -f $IMAGE ]; then
+	exit 0
+else
+	exit 1
+fi

2.7.6/densitree

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=densitree
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/generate_binaries.sh

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+#!/bin/bash
+
+TOOLS=(applauncher  beast  beauti  densitree  loganalyser  logcombiner  packagemanager  treeannotator)
+
+cat << EOF > template
+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=TOOL_NAME
+DIRECTORY=\$(dirname \$0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in "${STORAGES[@]}"
+do
+  	if [ -d "$STORAGE" ]; then
+		OPTIONS=$OPTIONS" -B $STORAGE"
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=$OPTIONS" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=$OPTIONS" -B /bil"
+fi
+
+singularity exec \$OPTIONS \$DIRECTORY/singularity-\$PACKAGE-\$VERSION.sif \$TOOL "\$@"
+EOF
+
+for TOOL in "${TOOLS[@]}"
+do
+	echo "* "$TOOL
+        cp template $TOOL
+	sed -i "s/TOOL_NAME/$TOOL/g" $TOOL
+	chmod +x $TOOL
+done
+
+rm -f template

2.7.6/loganalyser

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=loganalyser
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/logcombiner

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=logcombiner
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/modulefile.lua

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+--
+-- BEAST2 2.7.6 modulefile
+--
+-- "URL: https://www.psc.edu/resources/software"
+-- "Category: Utilities"
+-- "Description: BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences."
+-- "Keywords: singularity bioinformatics"
+
+whatis("Name: BEAST2-cli")
+whatis("Version: 2.7.6")
+whatis("Category: Utilities")
+whatis("URL: https://www.psc.edu/resources/software")
+whatis("Description: BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences..")
+whatis("Keywords: singularity utilities")
+
+help([[
+BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
+
+To load the module, type
+
+> module load BEAST2/2.7.6
+
+To unload the module, type
+
+> module unload BEAST2/2.7.6
+
+Tools included in this module are
+
+* beast
+* beauti
+* densitree
+* loganalyser
+* logcombiner
+* packagemanager
+* treeannotator
+]])
+
+local package = "BEAST2"
+local version = "2.7.6"
+local base    = pathJoin("/opt/packages",package,version)
+prepend_path("PATH", base)

2.7.6/packagemanager

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=packagemanager
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

2.7.6/rbuild.sh

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+#!/bin/bash
+
+IMAGE=singularity-BEAST2-2.7.6.sif
+DEFINITION=Singularity
+
+if [ -f $IMAGE ]; then
+	rm -fv $IMAGE
+fi
+
+singularity build --remote $IMAGE $DEFINITION
+
+if [ -f $IMAGE ]; then
+	exit 0
+else
+	exit 1
+fi

2.7.6/test.sh

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+#!/bin/bash
+
+set -x
+
+tree .

2.7.6/treeannotator

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+#!/bin/bash
+
+VERSION=2.7.6
+PACKAGE=BEAST2
+TOOL=treeannotator
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /local)
+
+OPTIONS=""
+for STORAGE in ""
+do
+  	if [ -d "" ]; then
+		OPTIONS=" -B "
+        fi
+done
+
+if id | grep -q hubmap && [ -d "/hive" ]; then
+	OPTIONS=" -B /hive"
+fi
+
+if id | grep -q bil && [ -d "/bil" ]; then
+	OPTIONS=" -B /bil"
+fi
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"