Remove all other definition files
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>julia_bam-readcounts 1.0.0_1.6.3
parent
f94009dd24
commit
35adec6f84
GPG Key ID:
139C07724802BC5D
@ -1,37 +0,0 @@
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# Assembly Improvement
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[](https://github.com/MillironX/singularity-builds/tree/master/assembly_improvement)
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[](https://github.com/sanger-pathogens/assembly_improvement)
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[](https://cloud.sylabs.io/library/millironx/default/assembly_improvement)
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[](https://github.com/sanger-pathogens/assembly_improvement/blob/master/README.md)
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[](https://www.centos.org/)
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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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## Tools installed
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### SSPACE
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- `SSPACE_Basic.pl`
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### GapFiller
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- `GapFiller`
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### Abacas
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- `abacas.pl`
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### SGA
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- `sga`
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### improve_assembly
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- `improve_assembly`
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- `diginorm_with_khmer`
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- `fill_gaps_with_gapfiller`
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- `order_contigs_with_abacas`
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- `read_correction_with_sga`
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- `scaffold_with_sspace`
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@ -1,173 +0,0 @@
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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 which -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 "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 1.160490
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SingularityDefinitionVersion 2
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%help
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Assembly Improvement
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====================
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Take in an assembly in FASTA format, reads in FASTQ format, and make the
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assembly better by scaffolding and gap filling.
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**NOTE:** When using this container, **do not** use options that point to the
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paths of binaries. These have already been included in the container, and
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shims are setup to point to the containerized binaries already.
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E.g. `improve_assembly` is shimmed to execute
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`improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@"`,
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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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@ -1,16 +0,0 @@
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# CliqueSNV
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[](https://github.com/MillironX/singularity-builds/tree/master/clique-snv)
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[](https://github.com/vtsyvina/CliqueSNV)
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[](https://cloud.sylabs.io/library/millironx/default/clique-snv)
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[](https://github.com/vtsyvina/CliqueSNV/blob/master/README.md)
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[](https://www.alpinelinux.org/)
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CliqueSNV can identify minority haplotypes based on extracting pairs of statistically linked mutations from noisy reads.
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## Tools installed
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### CliqueSNV
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- `java`
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- `clique-snv` as alias for `java -jar clique-snv.jar ...`
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@ -1,57 +0,0 @@
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Bootstrap: library
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From: default/alpine:3.14.0
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%post
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# Install java
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apk add --no-cache openjdk8 bash
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# Make versioning easier
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CLIQUE_VERSION=2.0.2
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cd /opt
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wget https://github.com/vtsyvina/CliqueSNV/archive/refs/tags/$CLIQUE_VERSION.tar.gz -O cliquesnv.tar.gz
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tar xvzf cliquesnv.tar.gz
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rm cliquesnv.tar.gz
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cd
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{
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echo "#!/bin/bash"
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echo "java -jar /opt/CliqueSNV-$CLIQUE_VERSION/clique-snv.jar \"\$@\""
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} > /usr/bin/clique-snv
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chmod +x /usr/bin/clique-snv
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%test
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test_command () {
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if ! command -v "${1}"; then
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echo "command ${1} not found!"
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export FAILED_TESTS=1
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fi
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}
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test_command bash
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test_command ps
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test_command java
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test_command clique-snv
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%runscript
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clique-snv "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 2.0.2
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SingularityDefinitionVersion 1
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%help
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CliqueSNV
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=========
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CliqueSNV can identify minority haplotypes based on extracting pairs of
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statistically linked mutations from noisy reads.
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For more help, see
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- <https://github.com/vtsyvina/CliqueSNV>
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- <https://github.com/MillironX/singularity-builds>
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@ -1,13 +0,0 @@
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# HTSLib
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[](https://github.com/MillironX/singularity-builds/tree/master/htslib)
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[](https://github.com/samtools/htslib)
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[](https://cloud.sylabs.io/library/millironx/default/htslib)
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[](https://www.htslib.org/)
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[](https://www.alpinelinux.org/)
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HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.
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## Tools installed
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none
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@ -1,57 +0,0 @@
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Bootstrap: library
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From: default/alpine:3.14.0
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%post
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# Get the actual dependencies
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apk add --no-cache zlib bash libcurl
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# Get the build dependencies
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apk add --no-cache --virtual .build-deps musl-dev g++ make zlib-dev bzip2-dev xz-dev curl-dev
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# Make versioning easier
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HTSLIB_VERSION='1.13'
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# Download the source tarball and build
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cd /tmp || exit 1
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wget https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2
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tar xjvf htslib-$HTSLIB_VERSION.tar.bz2
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cd htslib-$HTSLIB_VERSION || exit 1
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make && make install
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cd .. || exit 1
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rm -rf htslib-$SAMTOOLS_VERSION*
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cd || exit 1
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# Cleanup build packages
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apk del --no-cache .build-deps
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%test
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test_command () {
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if ! command -v "${1}"; then
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echo "command ${1} not found!"
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export FAILED_TESTS=1
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fi
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}
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test_command bash
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test_command ps
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 1.13
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SingularityDefinitionVersion 2
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%help
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HTSlib
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======
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HTSlib is an implementation of a unified C library for accessing common file
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formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
|
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and is the core library used by samtools and bcftools.
|
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|
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For more help, see
|
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- <https://www.htslib.org>
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- <https://github.com/MillironX/singularity-builds>
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@ -1,5 +0,0 @@
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FROM julia:1.6.2-alpine
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RUN apk add --no-cache bash
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CMD ["julia"]
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@ -1,15 +0,0 @@
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# Julia
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[](https://github.com/MillironX/singularity-builds/tree/master/julia)
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[](https://github.com/JuliaLang/julia)
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[](https://cloud.sylabs.io/library/millironx/default/assembly_improvement)
|
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[](https://docs.julialang.org/en/v1.6.2/)
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[](https://www.alpinelinux.org/)
|
||||
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Julia is a high-level dynamic programming language designed to address the needs of high-performance numerical analysis and computational science. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.
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## Tools installed
|
||||
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### Julia
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- `julia`
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@ -1,85 +0,0 @@
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Bootstrap: library
|
||||
From: default/alpine:3.14.0
|
||||
|
||||
%post
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||||
# Install dependencies
|
||||
apk add --no-cache bash
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apk add --no-cache --virtual .build-deps gnupg curl
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# Make our lives easier by declaring some constants
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||||
export JULIA_GPG="3673DF529D9049477F76B37566E3C7DC03D6E495"
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export JULIA_VERSION="1.6.2"
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export JULIA_PATH=/usr/local/julia
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export PATH=$JULIA_PATH/bin:$PATH
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export tarArch='x86_64'
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export dirArch='x64'
|
||||
export sha256='5ff279bc733a99a9582fd9b39eb3d18a3fa77b9d3d2733039279a250c8c5d49c'
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||||
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||||
# Download Julia
|
||||
export folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"
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curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/musl/${dirArch}/${folder}/julia-${JULIA_VERSION}-musl-${tarArch}.tar.gz.asc"
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curl -fL -o julia.tar.gz "https://julialang-s3.julialang.org/bin/musl/${dirArch}/${folder}/julia-${JULIA_VERSION}-musl-${tarArch}.tar.gz"
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||||
# Security check step 1: verify via sha256
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echo "${sha256} *julia.tar.gz" | sha256sum -c -
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# Security check step 2: verify via GPG
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||||
export GNUPGHOME="$(mktemp -d)"
|
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gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$JULIA_GPG"
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gpg --batch --verify julia.tar.gz.asc julia.tar.gz
|
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command -v gpgconf > /dev/null && gpgconf --kill all
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||||
rm -rf "$GNUPGHOME" julia.tar.gz.asc
|
||||
|
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# Extract Julia
|
||||
mkdir "$JULIA_PATH"
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tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1
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||||
rm julia.tar.gz
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||||
# Cleanup build dependencies
|
||||
apk del --no-cache .build-deps
|
||||
|
||||
%environment
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||||
export JULIA_PATH=/usr/local/julia
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export PATH=$JULIA_PATH/bin:$PATH
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|
||||
%test
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||||
cat << "EOF" > /tmp/singularity-test.sh
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#!/bin/bash
|
||||
CMDS=('bash' 'ps' 'julia')
|
||||
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
|
||||
EOF
|
||||
chmod +x /tmp/singularity-test.sh
|
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bash /tmp/singularity-test.sh
|
||||
|
||||
|
||||
%runscript
|
||||
julia "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion v1.6.2
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
Julia
|
||||
=====
|
||||
|
||||
Julia is a high-level dynamic programming language designed to address the
|
||||
needs of high-performance numerical analysis and computational science. It
|
||||
provides a sophisticated compiler, distributed parallel execution, numerical
|
||||
accuracy, and an extensive mathematical function library.
|
||||
Source: GitHub (<https://github.com/topics/julia>)
|
||||
|
||||
For more help, see
|
||||
- <https://julialang.org>
|
||||
- <https://github.com/JuliaLang/julia>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
@ -1,27 +0,0 @@
|
||||
# minimap2 (plus goodies)
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/minimap_plus)
|
||||
[](https://github.com/lh3/minimap2)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/minimap_plus)
|
||||
[](https://lh3.github.io/minimap2/)
|
||||
[](https://www.alpinelinux.org/)
|
||||
|
||||
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### minimap2
|
||||
|
||||
- `minimap2`
|
||||
|
||||
### samtools
|
||||
|
||||
- `samtools`
|
||||
|
||||
### Perl
|
||||
|
||||
- `perl`
|
||||
|
||||
### samclip
|
||||
|
||||
- `samclip`
|
||||
@ -1,74 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: millironx/default/samtools:1.13
|
||||
|
||||
%post
|
||||
# Get the actual dependencies
|
||||
apk add --no-cache perl
|
||||
|
||||
# Get the build dependencies
|
||||
apk add --no-cache --virtual .build-deps musl-dev g++ make zlib-dev
|
||||
|
||||
# Part 1: Install minimap2
|
||||
# ========================
|
||||
|
||||
# Make versioning easier
|
||||
MINIMAP2_VERSION='2.22'
|
||||
|
||||
# Download the source tarball and build
|
||||
cd /tmp || exit 1
|
||||
wget https://github.com/lh3/minimap2/releases/download/v$MINIMAP2_VERSION/minimap2-$MINIMAP2_VERSION.tar.bz2
|
||||
tar xjvf minimap2-$MINIMAP2_VERSION.tar.bz2
|
||||
cd minimap2-$MINIMAP2_VERSION || exit 1
|
||||
make
|
||||
install -D -m 0755 minimap2 -t /usr/bin
|
||||
cd .. || exit 1
|
||||
rm -rf minimap2-$MINIMAP2_VERSION*
|
||||
cd || exit 1
|
||||
|
||||
# Part 2: Install samclip
|
||||
SAMCLIP_VERSION='0.4.0'
|
||||
cd /usr/bin || exit 1
|
||||
wget https://raw.githubusercontent.com/tseemann/samclip/v$SAMCLIP_VERSION/samclip
|
||||
chmod a+x samclip
|
||||
cd || exit 1
|
||||
|
||||
# Cleanup build packages
|
||||
apk del --no-cache .build-deps
|
||||
|
||||
%test
|
||||
test_command () {
|
||||
if ! command -v "${1}"; then
|
||||
echo "command ${1} not found!"
|
||||
export FAILED_TESTS=1
|
||||
fi
|
||||
}
|
||||
|
||||
test_command bash
|
||||
test_command ps
|
||||
test_command samtools
|
||||
test_command minimap2
|
||||
test_command samclip
|
||||
|
||||
if [ -n "$FAILED_TESTS" ]; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
minimap2 "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion 2.22
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
minimap2
|
||||
========
|
||||
|
||||
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
|
||||
sequences against a large reference database.
|
||||
|
||||
For more help, see
|
||||
- <https://lh3.github.io/minimap2/>
|
||||
- <https://github.com/lh3/minimap2>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
@ -1,17 +0,0 @@
|
||||
# pigz
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/pigz)
|
||||
[](https://www.zlib.net/pigz/)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/pigz)
|
||||
[](https://www.zlib.net/pigz/pigz.pdf)
|
||||
[](https://www.centos.org/)
|
||||
|
||||
pigz, which stands for parallel implementation of gzip, is a fully functional
|
||||
replacement for gzip that exploits multiple processors and multiple cores to the
|
||||
hilt when compressing data.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### pigz
|
||||
|
||||
- `pigz`
|
||||
@ -1,32 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: default/centos:latest
|
||||
|
||||
%post
|
||||
dnf install pigz procps-ng -y
|
||||
|
||||
%test
|
||||
if [ ! "$(command -v pigz)" ]; then
|
||||
echo "command julia not found!"
|
||||
FAILED_TESTS="TRUE"
|
||||
fi
|
||||
|
||||
if [ ! "$(command -v bash)" ]; then
|
||||
echo "command bash not found!"
|
||||
FAILED_TESTS="TRUE"
|
||||
fi
|
||||
|
||||
if [ ! "$(command -v ps)" ]; then
|
||||
echo "command ps not found!"
|
||||
FAILED_TESTS="TRUE"
|
||||
fi
|
||||
|
||||
if [ -n "$FAILED_TESTS" ]; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
pigz "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
Version v2.3.1
|
||||
@ -1,17 +0,0 @@
|
||||
# Ray
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/ray)
|
||||
[](https://github.com/sebhtml/ray)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/ray)
|
||||
[](http://denovoassembler.sourceforge.net/)
|
||||
[](https://ubuntu.com/)
|
||||
|
||||
Ray is a parallel de novo genome assembler that utilises the message-passing
|
||||
interface everywhere and is implemented using peer-to-peer communication.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### Ray
|
||||
|
||||
- `mpiexec`
|
||||
- `Ray`
|
||||
@ -1,22 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: default/ubuntu:20.04
|
||||
|
||||
%post
|
||||
apt-get -y update
|
||||
apt-get -y --no-install-recommends install software-properties-common
|
||||
add-apt-repository universe
|
||||
apt-get -y update
|
||||
apt-get -y --no-install-recommends install ray
|
||||
|
||||
%test
|
||||
if [ ! "$(command -v Ray)" ]; then
|
||||
echo "command Ray not found!"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
mpiexec --use-hwthread-cpus Ray "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
Version v2.3.1
|
||||
@ -1,15 +0,0 @@
|
||||
# Samtools
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/samtools)
|
||||
[](https://github.com/samtools/samtools)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/samtools)
|
||||
[](https://www.htslib.org/doc/samtools.html)
|
||||
[](https://www.alpinelinux.org/)
|
||||
|
||||
Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### samtools
|
||||
|
||||
- `samtools`
|
||||
@ -1,63 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: default/alpine:3.14.0
|
||||
|
||||
%post
|
||||
# Get the actual dependencies
|
||||
apk add --no-cache ncurses libbz2 xz zlib bash
|
||||
|
||||
# Get the build dependencies
|
||||
apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
|
||||
|
||||
# Make versioning easier
|
||||
SAMTOOLS_VERSION='1.13'
|
||||
|
||||
# Download the source tarball and build
|
||||
cd /tmp || exit 1
|
||||
wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
|
||||
tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
|
||||
cd samtools-$SAMTOOLS_VERSION || exit 1
|
||||
./configure
|
||||
make && make install
|
||||
cd .. || exit 1
|
||||
rm -rf samtools-$SAMTOOLS_VERSION*
|
||||
cd || exit 1
|
||||
|
||||
# Cleanup build packages
|
||||
apk del --no-cache .build-deps
|
||||
|
||||
%test
|
||||
test_command () {
|
||||
if ! command -v "${1}"; then
|
||||
echo "command ${1} not found!"
|
||||
export FAILED_TESTS=1
|
||||
fi
|
||||
}
|
||||
|
||||
test_command bash
|
||||
test_command ps
|
||||
test_command samtools
|
||||
|
||||
if [ -n "$FAILED_TESTS" ]; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
samtools "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion 1.13
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
Samtools
|
||||
========
|
||||
|
||||
Samtools is a set of utilities that manipulate alignments in the SAM
|
||||
(Sequence Alignment/Map), BAM, and CRAM formats. It converts between the
|
||||
formats, does sorting, merging and indexing, and can retrieve reads in any
|
||||
regions swiftly.
|
||||
|
||||
For more help, see
|
||||
- <https://www.htslib.org/doc/samtools.html>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
@ -1,18 +0,0 @@
|
||||
# ShoRAH
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/shorah)
|
||||
[](https://github.com/cbg-ethz/shorah)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/shorah)
|
||||
[](https://github.com/cbg-ethz/shorah)
|
||||
[](https://www.alpinelinux.org/)
|
||||
|
||||
ShoRAH is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### ShoRAH
|
||||
|
||||
- `shorah`
|
||||
- `b2w`
|
||||
- `diri_sampler`
|
||||
- `fil`
|
||||
@ -1,71 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: millironx/default/htslib:1.13
|
||||
|
||||
%post
|
||||
# Install dependencies
|
||||
apk add --no-cache python3 libcurl
|
||||
|
||||
# Install build dependencies
|
||||
apk add --no-cache --virtual .build-deps py-pip g++ musl-dev make python3-dev boost-dev curl-dev
|
||||
|
||||
# Install python package dependencies
|
||||
pip install --no-cache-dir biopython==1.79 numpy==1.21.2
|
||||
|
||||
# Make versioning easier
|
||||
SHORAH_VERSION=1.99.2
|
||||
|
||||
# Download the source tarball and build
|
||||
cd /tmp || exit 1
|
||||
wget https://github.com/cbg-ethz/shorah/releases/download/v$SHORAH_VERSION/shorah-$SHORAH_VERSION.tar.bz2 -O shorah-$SHORAH_VERSION.tar.bz2
|
||||
tar xjvf shorah-$SHORAH_VERSION.tar.bz2
|
||||
cd shorah-$SHORAH_VERSION
|
||||
./configure
|
||||
make
|
||||
make install
|
||||
cd .. || exit 1
|
||||
rm -rf shorah-$SHORAH_VERSION*
|
||||
cd || exit 1
|
||||
|
||||
# Cleanup build packages
|
||||
apk del --no-cache .build-deps
|
||||
|
||||
%test
|
||||
test_command () {
|
||||
if ! command -v "${1}"; then
|
||||
echo "command ${1} not found!"
|
||||
export FAILED_TESTS=1
|
||||
fi
|
||||
}
|
||||
|
||||
test_command bash
|
||||
test_command ps
|
||||
test_command shorah
|
||||
test_command b2w
|
||||
test_command diri_sampler
|
||||
test_command fil
|
||||
|
||||
if [ -n "$FAILED_TESTS" ]; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
shorah "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion 2.0.2
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
ShoRAH
|
||||
======
|
||||
|
||||
ShoRAH is an open source project for the analysis of next generation
|
||||
sequencing data. It is designed to analyse genetically heterogeneous samples.
|
||||
Its tools are written in different programming languages and provide error
|
||||
correction, haplotype reconstruction and estimation of the frequency of the
|
||||
different genetic variants present in a mixed sample.
|
||||
|
||||
For more help, see
|
||||
- <http://cbg-ethz.github.io/shorah>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
@ -1,19 +0,0 @@
|
||||
# VarScan
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/varscan)
|
||||
[](https://github.com/dkoboldt/varscan)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/varscan)
|
||||
[](https://dkoboldt.github.io/varscan/)
|
||||
[](https://www.alpinelinux.org/)
|
||||
|
||||
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.
|
||||
|
||||
## Tools installed
|
||||
|
||||
### samtools
|
||||
|
||||
- `samtools`
|
||||
|
||||
### VarScan
|
||||
|
||||
- `varscan`
|
||||
@ -1,93 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: default/alpine:3.14.0
|
||||
|
||||
%post
|
||||
# Part 1: Install Samtools
|
||||
# ========================
|
||||
|
||||
# Get the actual dependencies
|
||||
apk add --no-cache ncurses libbz2 xz zlib
|
||||
|
||||
# Get the build dependencies
|
||||
apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
|
||||
|
||||
# Make versioning easier
|
||||
SAMTOOLS_VERSION='1.13'
|
||||
|
||||
# Download the source tarball and build
|
||||
cd /tmp || exit 1
|
||||
wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
|
||||
tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
|
||||
cd samtools-$SAMTOOLS_VERSION || exit 1
|
||||
./configure
|
||||
make && make install
|
||||
cd .. || exit 1
|
||||
rm -rf samtools-$SAMTOOLS_VERSION*
|
||||
cd || exit 1
|
||||
|
||||
# Cleanup build packages
|
||||
apk del --no-cache .build-deps
|
||||
|
||||
# Part 2: Install VarScan
|
||||
# ========================
|
||||
|
||||
# Install java
|
||||
apk add --no-cache openjdk8
|
||||
|
||||
# Make versioning easier
|
||||
VARSCAN_VERSION='v2.4.4'
|
||||
|
||||
# Download varscan
|
||||
wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar -O /opt/varscan.jar
|
||||
|
||||
# Create a shim for varscan
|
||||
echo "#!/bin/bash" > /usr/local/bin/varscan
|
||||
echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan
|
||||
chmod +x /usr/local/bin/varscan
|
||||
|
||||
# Part 3: Install Nextflow dependencies
|
||||
# =====================================
|
||||
apk add --no-cache bash
|
||||
|
||||
%test
|
||||
cat << "EOF" > /tmp/singularity-test.sh
|
||||
#!/bin/bash
|
||||
CMDS=('bash' 'ps' 'java' 'varscan' 'samtools')
|
||||
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
|
||||
EOF
|
||||
chmod +x /tmp/singularity-test.sh
|
||||
bash /tmp/singularity-test.sh
|
||||
|
||||
%runscript
|
||||
varscan "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion v2.4.4
|
||||
SingularityDefinitionVersion 2
|
||||
|
||||
%help
|
||||
VarScan
|
||||
=======
|
||||
|
||||
VarScan is a platform-independent mutation caller for targeted, exome, and
|
||||
whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM,
|
||||
Roche/454, and similar instruments. It can be used to detect different types
|
||||
of variation:
|
||||
- Germline variants (SNPs an dindels) in individual samples or pools of samples.
|
||||
- Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
|
||||
- Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
|
||||
- Somatic copy number alterations (CNAs) in tumor-normal exome data.
|
||||
|
||||
For more help, see
|
||||
- <https://dkoboldt.github.io/varscan/>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
@ -1,16 +0,0 @@
|
||||
# Velvet
|
||||
|
||||
[](https://github.com/MillironX/singularity-builds/tree/master/velvet)
|
||||
[](http://github.com/dzerbino/velvet/tree/master)
|
||||
[](https://cloud.sylabs.io/library/millironx/default/velvet)
|
||||
[](https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf)
|
||||
[](https://www.centos.org/)
|
||||
|
||||
Sequence assembler for very short reads
|
||||
|
||||
## Tools installed
|
||||
|
||||
### Velvet
|
||||
|
||||
- `velvetg`
|
||||
- `velveth`
|
||||
@ -1,49 +0,0 @@
|
||||
Bootstrap: library
|
||||
From: default/centos:latest
|
||||
|
||||
%post
|
||||
# Quiet perl down
|
||||
export LC_ALL=C
|
||||
|
||||
# Install package files
|
||||
dnf install dnf-plugins-core -y
|
||||
dnf copr enable millironx/velvet -y
|
||||
dnf install velvet-1.2.10 procps -y
|
||||
|
||||
# Clean up
|
||||
dnf remove dnf-plugins-core -y
|
||||
dnf autoremove -y
|
||||
dnf clean all
|
||||
|
||||
%environment
|
||||
export LC_ALL=C
|
||||
|
||||
%test
|
||||
# We can use bash notation here, since /bin/sh is symlinked to bash in CentOS
|
||||
CMDS=('bash' 'ps' 'velvetg' 'velveth')
|
||||
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
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion 1.2.10
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
Velvet
|
||||
======
|
||||
|
||||
Sequence assembler for very short reads
|
||||
|
||||
For more help, see
|
||||
- <https://www.ebi.ac.uk/~zerbino/velvet/>
|
||||
- <https://github.com/MillironX/velvet-copr>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
Loading…
Reference in New Issue