Bootstrap: library From: default/centos:latest %post # Quiet perl down export LC_ALL=C # Install package files: repositories dnf install dnf-plugins-core -y dnf install epel-release -y dnf config-manager --set-enabled PowerTools # Operating dependencies dnf --setopt=install_weak_deps=False install procps perl python3 which -y # Building dependencies dnf groupinstall 'Development Tools' -y dnf install perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y # Install SSPACE cd /opt || exit 1 git clone https://github.com/nsoranzo/sspace_basic.git cd sspace_basic || exit 1 git checkout 4fe5c # Not available as release tarball cd || exit 1 export PATH=$PATH:/opt/sspace_basic # Install GapFiller curl -L https://downloads.sourceforge.net/project/gapfiller/v2.1.2/gapfiller-2.1.2.tar.gz | tar xvz cd gapfiller-2.1.2 ./configure make && make install cd .. || exit 1 rm -rf gapfiller-2.1.2 # Install khmer pip3 install khmer # Install MUMmer curl -L https://github.com/mummer4/mummer/releases/download/v4.0.0rc1/mummer-4.0.0rc1.tar.gz | tar xvz cd mummer-4.0.0rc1 || exit 1 ./configure make && make install cd .. || exit 1 rm -rf mummer-4.0.0rc1 # SGA uses an old C++ standard, so all of its dependencies must be compiled # against that standard, too export CFLAGS=-std=gnu++03 export CXXFLAGS=-std=gnu++03 export CPPFLAGS=-std=gnu++03 # Install Google sparsehash (dependency for SGA) curl -L https://github.com/sparsehash/sparsehash/archive/refs/tags/sparsehash-2.0.4.tar.gz | tar xvz cd sparsehash-sparsehash-2.0.4 || exit 1 ./configure make && make install cd .. || exit 1 rm -rf sparsehash-sparsehash-2.0.4 # Install bamtools library (dependency for SGA) curl -L https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz | tar xvz cd bamtools-2.5.2 || exit 1 mkdir build && cd build || exit 1 # Dependency issue unique to RHEL/CentOS 8: https://github.com/ComplianceAsCode/content/issues/7016#issuecomment-845066366 dnf upgrade libarchive -y cmake .. make && make install cd ../.. || exit 1 rm -rf bamtools-2.5.2 # Install ruffus (dependency for SGA) pip3 install ruffus --upgrade # Install pysam (dependency for SGA) pip3 install pysam # Install SGA git clone https://github.com/jts/sga.git cd sga/src || exit 1 git checkout 229293b # Contains compiler-blocking bug fixes that are not in the release tarball ./autogen.sh ./configure --with-bamtools=/usr/local make && make install cd ../.. || exit 1 rm -rf sga # Unset the compiler flags export CFLAGS='' export CXXFLAGS='' export CPPFLAGS='' # QUASR is nowhere to be found, so skip installing it # Install assembly_improvement's dependencies cpanm -f Bio::AssemblyImprovement # Install an up-to-date version of assembly_improvement cd /opt || exit 1 curl -L https://github.com/sanger-pathogens/assembly_improvement/releases/download/v2021.01.04.08.24.00.726/Bio_AssemblyImprovement-2021.01.04.08.24.00.726.tar.gz | tar xvz export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin cd || exit 1 # Shim preloaded arguments into PATH IMPROVE_PREFIX=/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin SSPACE_PATH=/opt/sspace_basic/SSPACE_Basic.pl GF_PATH=/usr/local/bin/GapFiller ABACAS_PATH=/usr/local/bin/abacas.pl SGA_PATH=/usr/local/bin/sga cd /opt || exit 1 mkdir shims && cd shims || exit 1 echo "$IMPROVE_PREFIX/improve_assembly -s $SSPACE_PATH -g $GF_PATH -b $ABACAS_PATH \"\$@\"" > improve_assembly echo "$IMPROVE_PREFIX/diginorm_with_khmer -py /usr/bin/python3 \"\$@\"" > diginorm_with_khmer echo "$IMPROVE_PREFIX/fill_gaps_with_gapfiller -s $GF_PATH \"\$@\"" > fill_gaps_with_gapfiller echo "$IMPROVE_PREFIX/order_contigs_with_abacas -b $ABACAS_PATH \"\$@\"" > order_contigs_with_abacas echo "$IMPROVE_PREFIX/read_correction_with_sga -s $SGA_PATH \"\$@\"" > read_correction_with_sga echo "$IMPROVE_PREFIX/scaffold_with_sspace -s $SSPACE_PATH \"\$@\"" > scaffold_with_sspace echo "echo 'Error! QUASR is discontinued and not available in this container.'; exit 1" > remove_primers_with_quasr chmod +x ./* cd || exit 1 export PATH=/opt/shims:$PATH # Clean up dnf groupremove 'Development Tools' -y dnf remove perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y dnf autoremove -y dnf clean all %environment export LC_ALL=C export PATH=$PATH:/opt/sspace_basic export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin export PATH=/opt/shims:$PATH %test # We can use bash notation here, since /bin/sh is symlinked to bash in CentOS CMDS=('bash' 'ps' 'SSPACE_Basic.pl' 'GapFiller' 'abacas.pl' 'sga' 'improve_assembly' 'diginorm_with_khmer' 'fill_gaps_with_gapfiller' 'order_contigs_with_abacas' 'read_correction_with_sga' 'scaffold_with_sspace') for CMD in "${CMDS[@]}"; do if ! command -v "$CMD"; then echo "command $CMD not found!" FAILED_TESTS=1 fi done # Abort if a test failed if [ -n "$FAILED_TESTS" ]; then exit 1 fi %runscript /opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin/improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@" %labels Author 25492070+MillironX@users.noreply.github.com SoftwareVersion 1.160490 SingularityDefinitionVersion 2 %help Assembly Improvement ==================== Take in an assembly in FASTA format, reads in FASTQ format, and make the assembly better by scaffolding and gap filling. **NOTE:** When using this container, **do not** use options that point to the paths of binaries. These have already been included in the container, and shims are setup to point to the containerized binaries already. E.g. `improve_assembly` is shimmed to execute `improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@"`, so providing `-s`, `-g`, or `-b` will break the usage. For more help, see - -