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Add Sanger Pathogens' Assembly Improvement
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173
assembly_improvement/assembly_improvement.def
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173
assembly_improvement/assembly_improvement.def
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Bootstrap: library
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From: default/centos:latest
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%post
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# Quiet perl down
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export LC_ALL=C
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# Install package files: repositories
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dnf install dnf-plugins-core -y
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dnf install epel-release -y
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dnf config-manager --set-enabled PowerTools
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# Operating dependencies
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dnf --setopt=install_weak_deps=False install procps perl python3 -y
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# Building dependencies
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dnf groupinstall 'Development Tools' -y
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dnf install perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y
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# Install SSPACE
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cd /opt || exit 1
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git clone https://github.com/nsoranzo/sspace_basic.git
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cd sspace_basic || exit 1
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git checkout 4fe5c # Not available as release tarball
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cd || exit 1
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export PATH=$PATH:/opt/sspace_basic
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# Install GapFiller
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curl -L https://downloads.sourceforge.net/project/gapfiller/v2.1.2/gapfiller-2.1.2.tar.gz | tar xvz
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cd gapfiller-2.1.2
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./configure
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make && make install
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cd .. || exit 1
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rm -rf gapfiller-2.1.2
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# Install khmer
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pip3 install khmer
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# Install MUMmer
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curl -L https://github.com/mummer4/mummer/releases/download/v4.0.0rc1/mummer-4.0.0rc1.tar.gz | tar xvz
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cd mummer-4.0.0rc1 || exit 1
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./configure
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make && make install
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cd .. || exit 1
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rm -rf mummer-4.0.0rc1
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# SGA uses an old C++ standard, so all of its dependencies must be compiled
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# against that standard, too
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export CFLAGS=-std=gnu++03
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export CXXFLAGS=-std=gnu++03
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export CPPFLAGS=-std=gnu++03
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# Install Google sparsehash (dependency for SGA)
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curl -L https://github.com/sparsehash/sparsehash/archive/refs/tags/sparsehash-2.0.4.tar.gz | tar xvz
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cd sparsehash-sparsehash-2.0.4 || exit 1
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./configure
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make && make install
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cd .. || exit 1
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rm -rf sparsehash-sparsehash-2.0.4
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# Install bamtools library (dependency for SGA)
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curl -L https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz | tar xvz
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cd bamtools-2.5.2 || exit 1
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mkdir build && cd build || exit 1
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# Dependency issue unique to RHEL/CentOS 8: https://github.com/ComplianceAsCode/content/issues/7016#issuecomment-845066366
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dnf upgrade libarchive -y
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cmake ..
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make && make install
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cd ../.. || exit 1
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rm -rf bamtools-2.5.2
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# Install ruffus (dependency for SGA)
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pip3 install ruffus --upgrade
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# Install pysam (dependency for SGA)
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pip3 install pysam
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# Install SGA
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git clone https://github.com/jts/sga.git
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cd sga/src || exit 1
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git checkout 229293b # Contains compiler-blocking bug fixes that are not in the release tarball
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./autogen.sh
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./configure --with-bamtools=/usr/local
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make && make install
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cd ../.. || exit 1
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rm -rf sga
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# Unset the compiler flags
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export CFLAGS=''
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export CXXFLAGS=''
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export CPPFLAGS=''
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# QUASR is nowhere to be found, so skip installing it
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# Install assembly_improvement's dependencies
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cpanm -f Bio::AssemblyImprovement
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# Install an up-to-date version of assembly_improvement
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cd /opt || exit 1
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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
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export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
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cd || exit 1
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# Shim preloaded arguments into PATH
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IMPROVE_PREFIX=/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
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SSPACE_PATH=/opt/sspace_basic/SSPACE_Basic.pl
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GF_PATH=/usr/local/bin/GapFiller
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ABACAS_PATH=/usr/local/bin/abacas.pl
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SGA_PATH=/usr/local/bin/sga
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cd /opt || exit 1
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mkdir shims && cd shims || exit 1
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echo "$IMPROVE_PREFIX/improve_assembly -s $SSPACE_PATH -g $GF_PATH -b $ABACAS_PATH \"\$@\"" > improve_assembly
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echo "$IMPROVE_PREFIX/diginorm_with_khmer -py /usr/bin/python3 \"\$@\"" > diginorm_with_khmer
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echo "$IMPROVE_PREFIX/fill_gaps_with_gapfiller -s $GF_PATH \"\$@\"" > fill_gaps_with_gapfiller
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echo "$IMPROVE_PREFIX/order_contigs_with_abacas -b $ABACAS_PATH \"\$@\"" > order_contigs_with_abacas
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echo "$IMPROVE_PREFIX/read_correction_with_sga -s $SGA_PATH \"\$@\"" > read_correction_with_sga
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echo "$IMPROVE_PREFIX/scaffold_with_sspace -s $SSPACE_PATH \"\$@\"" > scaffold_with_sspace
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echo "echo 'Error! QUASR is discontinued and not available in this container.'; exit 1" > remove_primers_with_quasr
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chmod +x ./*
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cd || exit 1
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export PATH=/opt/shims:$PATH
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# Clean up
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dnf groupremove 'Development Tools' -y
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dnf remove perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y
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dnf autoremove -y
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dnf clean all
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%environment
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export LC_ALL=C
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export PATH=$PATH:/opt/sspace_basic
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export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
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export PATH=/opt/shims:$PATH
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%test
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# We can use bash notation here, since /bin/sh is symlinked to bash in CentOS
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CMDS=('bash' 'ps' 'SSPACE_Basic.pl' 'GapFiller' 'abacas.pl' 'sga' 'improve_assembly' 'diginorm_with_khmer' 'fill_gaps_with_gapfiller' 'order_contigs_with_abacas' 'read_correction_with_sga' 'scaffold_with_sspace')
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for CMD in "${CMDS[@]}"; do
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if ! command -v "$CMD"; then
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echo "command $CMD not found!"
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FAILED_TESTS=1
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fi
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done
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# Abort if a test failed
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%runscript
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/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 "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 1.160490
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SingularityDefinitionVersion 1
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%help
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Assembly Improvement
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====================
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Take in an assembly in FASTA format, reads in FASTQ format, and make the
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assembly better by scaffolding and gap filling.
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**NOTE:** When using this container, **do not** use options that point to the
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paths of binaries. These have already been included in the container, and
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shims are setup to point to the containerized binaries already.
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E.g. `improve_assembly` is shimmed to execute
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`improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@"`,
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so providing `-s`, `-g`, or `-b` will break the usage.
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For more help, see
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- <https://github.com/sanger-pathogens/assembly_improvement>
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- <https://github.com/MillironX/singularity-builds>
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