From 5e2ed4f14958b9253fdba5db9b5d90b3098d622d Mon Sep 17 00:00:00 2001 From: icaoberg Date: Wed, 29 May 2024 22:08:00 -0400 Subject: [PATCH] Added version 2.7.6 --- 2.7.6/Singularity | 26 +++++++++++++++++++++++ 2.7.6/applauncher | 26 +++++++++++++++++++++++ 2.7.6/beast | 26 +++++++++++++++++++++++ 2.7.6/beauti | 26 +++++++++++++++++++++++ 2.7.6/build.sh | 16 +++++++++++++++ 2.7.6/densitree | 26 +++++++++++++++++++++++ 2.7.6/generate_binaries.sh | 42 ++++++++++++++++++++++++++++++++++++++ 2.7.6/loganalyser | 26 +++++++++++++++++++++++ 2.7.6/logcombiner | 26 +++++++++++++++++++++++ 2.7.6/modulefile.lua | 41 +++++++++++++++++++++++++++++++++++++ 2.7.6/packagemanager | 26 +++++++++++++++++++++++ 2.7.6/rbuild.sh | 16 +++++++++++++++ 2.7.6/test.sh | 5 +++++ 2.7.6/treeannotator | 26 +++++++++++++++++++++++ 14 files changed, 354 insertions(+) create mode 100644 2.7.6/Singularity create mode 100755 2.7.6/applauncher create mode 100755 2.7.6/beast create mode 100755 2.7.6/beauti create mode 100755 2.7.6/build.sh create mode 100755 2.7.6/densitree create mode 100755 2.7.6/generate_binaries.sh create mode 100755 2.7.6/loganalyser create mode 100755 2.7.6/logcombiner create mode 100644 2.7.6/modulefile.lua create mode 100755 2.7.6/packagemanager create mode 100755 2.7.6/rbuild.sh create mode 100755 2.7.6/test.sh create mode 100755 2.7.6/treeannotator diff --git a/2.7.6/Singularity b/2.7.6/Singularity new file mode 100644 index 0000000..085aa15 --- /dev/null +++ b/2.7.6/Singularity @@ -0,0 +1,26 @@ +Bootstrap: docker +From: ubuntu:20.04 + +%labels + AUTHOR icaoberg + EMAIL icaoberg@psc.edu + SUPPORT help@psc.edu + 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=$PATH:/opt/beast/bin + +%post + apt update + apt install -y default-jdk + apt install -y libxext6 libxrender1 libxtst6 libxi6 + cd /opt + tar -xvf BEAST.v2.7.6.Linux.x86.tgz && rm -fv BEAST.v2.7.6.Linux.x86.tgz + +%runscript + /opt/beast/bin/applauncher diff --git a/2.7.6/applauncher b/2.7.6/applauncher new file mode 100755 index 0000000..7020fe2 --- /dev/null +++ b/2.7.6/applauncher @@ -0,0 +1,26 @@ +#!/bin/bash + +VERSION=2.7.6 +PACKAGE=BEAST2 +TOOL=applauncher +DIRECTORY=$(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 $TOOL "$@" diff --git a/2.7.6/beast b/2.7.6/beast new file mode 100755 index 0000000..1b9195a --- /dev/null +++ b/2.7.6/beast @@ -0,0 +1,26 @@ +#!/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 $TOOL "$@" diff --git a/2.7.6/beauti b/2.7.6/beauti new file mode 100755 index 0000000..a93e75a --- /dev/null +++ b/2.7.6/beauti @@ -0,0 +1,26 @@ +#!/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 $TOOL "$@" diff --git a/2.7.6/build.sh b/2.7.6/build.sh new file mode 100755 index 0000000..1acd42a --- /dev/null +++ b/2.7.6/build.sh @@ -0,0 +1,16 @@ +#!/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 $IMAGE ]; then + exit 0 +else + exit 1 +fi diff --git a/2.7.6/densitree b/2.7.6/densitree new file mode 100755 index 0000000..bf3db98 --- /dev/null +++ b/2.7.6/densitree @@ -0,0 +1,26 @@ +#!/bin/bash + +VERSION=2.7.6 +PACKAGE=BEAST2 +TOOL=densitree +DIRECTORY=$(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 $TOOL "$@" diff --git a/2.7.6/generate_binaries.sh b/2.7.6/generate_binaries.sh new file mode 100755 index 0000000..96992a5 --- /dev/null +++ b/2.7.6/generate_binaries.sh @@ -0,0 +1,42 @@ +#!/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 $TOOL +done + +rm -f template diff --git a/2.7.6/loganalyser b/2.7.6/loganalyser new file mode 100755 index 0000000..506b13e --- /dev/null +++ b/2.7.6/loganalyser @@ -0,0 +1,26 @@ +#!/bin/bash + +VERSION=2.7.6 +PACKAGE=BEAST2 +TOOL=loganalyser +DIRECTORY=$(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 $TOOL "$@" diff --git a/2.7.6/logcombiner b/2.7.6/logcombiner new file mode 100755 index 0000000..d99938b --- /dev/null +++ b/2.7.6/logcombiner @@ -0,0 +1,26 @@ +#!/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 $TOOL "$@" diff --git a/2.7.6/modulefile.lua b/2.7.6/modulefile.lua new file mode 100644 index 0000000..7a72df1 --- /dev/null +++ b/2.7.6/modulefile.lua @@ -0,0 +1,41 @@ +-- +-- 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) diff --git a/2.7.6/packagemanager b/2.7.6/packagemanager new file mode 100755 index 0000000..8ead169 --- /dev/null +++ b/2.7.6/packagemanager @@ -0,0 +1,26 @@ +#!/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 $TOOL "$@" diff --git a/2.7.6/rbuild.sh b/2.7.6/rbuild.sh new file mode 100755 index 0000000..47a238e --- /dev/null +++ b/2.7.6/rbuild.sh @@ -0,0 +1,16 @@ +#!/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 $IMAGE ]; then + exit 0 +else + exit 1 +fi diff --git a/2.7.6/test.sh b/2.7.6/test.sh new file mode 100755 index 0000000..2552134 --- /dev/null +++ b/2.7.6/test.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +set -x + +tree . diff --git a/2.7.6/treeannotator b/2.7.6/treeannotator new file mode 100755 index 0000000..93b98dc --- /dev/null +++ b/2.7.6/treeannotator @@ -0,0 +1,26 @@ +#!/bin/bash + +VERSION=2.7.6 +PACKAGE=BEAST2 +TOOL=treeannotator +DIRECTORY=$(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 $TOOL "$@"