From 3c256af029b4095311a1b1ec2d567a42e56bf1bb Mon Sep 17 00:00:00 2001
From: galaxy <patrick@plealog.com>
Date: Tue, 3 Oct 2023 12:38:35 +0000
Subject: [PATCH] use debian 11

---
 singularity/Singularity       | 61 ++++++++++++++++-------------------
 singularity/Singularity.local |  5 ++-
 2 files changed, 30 insertions(+), 36 deletions(-)

diff --git a/singularity/Singularity b/singularity/Singularity
index ff37554..90586ce 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -6,38 +6,32 @@
 # #############################################################################
 
 Bootstrap : docker
-From: ubuntu:18.04
+From: debian:11-slim
 
 %post
 	BDM_VERSION=5.0.0
-        #apt update
-        # software-properties-common required to install Java Runtime
-        # libbz2 libidn are required by blast tools included in BeeDeeM.
-        # libxext libxrender libxtst libxi are required by Bioinformatics-Core-API included 
-        #    in BeeDeeM and BeeDeeM-Tools.
-        # bash is required when running this image by Nextflow pipelines.
-        # wget is required to install some banks (e.g. GeneOntology).
-	# unzip is required to deploy BeeDeeM archive
-	# openssh-server is required to submit jobs on cluster through ssh connection
-        apt-get -y update
-        apt-get -y install software-properties-common bzip2 libidn11 bash wget libxext6 libxrender1 libxtst6 libxi6 unzip openssh-server
-
-        # Java
-        add-apt-repository ppa:ts.sch.gr/ppa \
-          && echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections \
-          && echo debconf shared/accepted-oracle-license-v1-1 seen true | debconf-set-selections \
-          && apt-get update \
-          && apt-get -y install oracle-java8-installer \
-          && apt-get -y install oracle-java8-set-default \
-          && apt-get clean all \
-          && rm -rf /var/lib/apt/lists/*
-        cd /usr/lib/jvm/java-8-oracle
-        rm -rf bin include lib man *.zip
-
-	# Get BeeDeeM from latest release
-	mkdir -p /opt/beedeem/tmp-install
-	cd /opt/beedeem/tmp-install
-	wget https://github.com/pgdurand/BeeDeeM/releases/download/v${BDM_VERSION}/beedeem-${BDM_VERSION}-distrib.zip
+	BDMT_VERSION=2.1.2
+	
+	# software-properties-common required to install Java Runtime
+	# libbz2 libidn are required by blast tools included in BeeDeeM.
+	# libxext libxrender libxtst libxi are required by Bioinformatics-Core-API included 
+	#    in BeeDeeM and BeeDeeM-Tools.
+	# bash is required when running this image by Nextflow pipelines.
+	# wget is required to install some banks (e.g. GeneOntology).
+	apt-get -y update
+	apt-get -y install gawk openssh-client software-properties-common bzip2 libidn11 bash wget libxext6 libxrender1 libxtst6 libxi6 unzip
+	
+	# Java
+	# See https://www.oracle.com/java/technologies/downloads/#java17
+        cd /opt
+        wget https://download.oracle.com/java/17/latest/jdk-17_linux-x64_bin.deb
+	apt install -y /opt/jdk-17_linux-x64_bin.deb
+	rm jdk-17_linux-x64_bin.deb
+	
+	# Get BeeDeeM from latest local release
+        mkdir -p /opt/beedeem/tmp-install
+        cd /opt/beedeem/tmp-install
+        wget https://github.com/pgdurand/BeeDeeM/releases/download/v${BDM_VERSION}/beedeem-${BDM_VERSION}-distrib.zip
 	
 	# Unpack BeeDeeM to /opt/beedeem
 	unzip beedeem-${BDM_VERSION}-distrib.zip
@@ -47,8 +41,8 @@ From: ubuntu:18.04
 	
 	# Do a little configuration
 	cp scripts/bdm.sh ./bdm
-        sed -i 's/@KL_WORKING_DIR@/\/beedeem-wk/g' bdm
-        sed -i 's/@JAVA_ARGS@/-Xms128M -Xmx2048M -Djava.io.tmpdir=\$KL_WORKING_DIR -DKL_LOG_TYPE=console/g' bdm
+	sed -i 's/@KL_WORKING_DIR@/\/beedeem-wk/g' bdm
+	sed -i 's/@JAVA_ARGS@/-Xms128M -Xmx2048M -Djava.io.tmpdir=\$KL_WORKING_DIR -DKL_LOG_TYPE=console/g' bdm
 	cp scripts/dbms.config conf
 	sed -i 's/@BIOBASE_ROOTDIR@/\/beedeem-db/g' conf/dbms.config
 	chmod +x bdm
@@ -57,7 +51,7 @@ From: ubuntu:18.04
 	chmod +x /opt/beedeem/conf/scripts/scheduler/*.sh
 	cd /opt/beedeem/external/bin && rm -rf macos windows
 
-	BDMT_VERSION=2.1.2
+	# Get BeeDeeM-Tools from latest local release
 	cd /opt
 	mkdir beedeem-tools
 	cd beedeem-tools
@@ -67,6 +61,7 @@ From: ubuntu:18.04
 	rm beedeem-tools-${BDMT_VERSION}.tar
 	chmod +x *.sh
 
-
 %environment
 	export PATH="/opt/beedeem:/opt/beedeem-tools:$PATH"
+	
+
diff --git a/singularity/Singularity.local b/singularity/Singularity.local
index ac797bb..7ed1bff 100644
--- a/singularity/Singularity.local
+++ b/singularity/Singularity.local
@@ -14,7 +14,7 @@
 # #############################################################################
 
 Bootstrap : docker
-From: debian:12-slim
+From: debian:11-slim
 
 %files
 	../distrib/beedeem-5.0.1-distrib.zip /opt
@@ -30,14 +30,13 @@ From: debian:12-slim
 	# bash is required when running this image by Nextflow pipelines.
 	# wget is required to install some banks (e.g. GeneOntology).
 	apt-get -y update
-	apt-get -y install gawk openssh-client software-properties-common bzip2 libidn12 bash wget libxext6 libxrender1 libxtst6 libxi6 unzip
+	apt-get -y install gawk openssh-client software-properties-common bzip2 libidn11 bash wget libxext6 libxrender1 libxtst6 libxi6 unzip
 	
 	# Java
 	# See https://www.oracle.com/java/technologies/downloads/#java17
         cd /opt
         wget https://download.oracle.com/java/17/latest/jdk-17_linux-x64_bin.deb
 	apt install -y /opt/jdk-17_linux-x64_bin.deb
-	update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk-17/bin/java 1
 	rm jdk-17_linux-x64_bin.deb
 	
 	# Get BeeDeeM from latest local release