use debian 11

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"
+
+

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