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* adding parsnp 2.0.4 * Copy license from builder * Removed explicit LICENSE copy
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| Original file line number | Diff line number | Diff line change |
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| ARG PARSNP_VER="2.0.4" | ||
| ARG HARVEST_VER="1.3" | ||
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| FROM ubuntu:jammy as builder | ||
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| ARG PARSNP_VER | ||
| ARG HARVEST_VER | ||
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| ARG RAXML_VER="8.2.12" | ||
| ARG FASTTREE_VER="2.1.11" | ||
| ARG MASH_VER="2.3" | ||
| ARG FASTANI_VER="1.34" | ||
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| # Update package index, install packages (ParSNP basic dependencies and packages needed to build from source) | ||
| RUN apt-get update && apt-get install -y \ | ||
| autoconf \ | ||
| make \ | ||
| build-essential \ | ||
| capnproto \ | ||
| libcapnp-dev \ | ||
| libgsl0-dev \ | ||
| libprotobuf-dev \ | ||
| libssl-dev \ | ||
| libtool \ | ||
| protobuf-compiler \ | ||
| libsqlite3-dev \ | ||
| wget \ | ||
| zlib1g-dev \ | ||
| python3 \ | ||
| python3-pip \ | ||
| unzip | ||
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| # Add /usr/lib to the library path so Mash and HarvestTools can find the capnp libraries | ||
| ENV LD_LIBRARY_PATH="/usr/lib:/usr/local/lib" | ||
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| # Move some static libraries that Mash and HarvestTools demand to where they want to see them | ||
| RUN cp /usr/lib/x86_64-linux-gnu/libprotobuf.a /usr/lib/ && \ | ||
| cp /usr/lib/x86_64-linux-gnu/libcapnp.a /usr/lib/ && \ | ||
| cp /usr/lib/x86_64-linux-gnu/libkj.a /usr/lib/ | ||
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| RUN pip3 install numpy | ||
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| # install fasttree | ||
| # ParSNP expects the FastTree executable to be called 'fasttree' | ||
| RUN wget -q http://www.microbesonline.org/fasttree/FastTree && \ | ||
| chmod +x FastTree && \ | ||
| mv FastTree /usr/local/bin/fasttree | ||
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| # Install RAxML: https://cme.h-its.org/exelixis/resource/download/NewManual.pdf | ||
| RUN wget -q https://github.com/stamatak/standard-RAxML/archive/refs/tags/v$RAXML_VER.tar.gz && \ | ||
| tar -xvf v$RAXML_VER.tar.gz && \ | ||
| cd standard-RAxML-$RAXML_VER && \ | ||
| make -f Makefile.AVX.PTHREADS.gcc && \ | ||
| cp /standard-RAxML-$RAXML_VER/raxmlHPC-PTHREADS-AVX /usr/local/bin/raxmlHPC-PTHREADS | ||
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| # Install Mash: https://github.com/marbl/Mash/blob/master/INSTALL.txt | ||
| RUN wget -q https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \ | ||
| tar -xf mash-Linux64-v${MASH_VER}.tar --no-same-owner && \ | ||
| rm -rf mash-Linux64-v${MASH_VER}.tar && \ | ||
| chown root:root /mash-Linux64-v${MASH_VER}/* | ||
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| # Install PhiPack: https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf | ||
| RUN wget -q https://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar.gz && \ | ||
| tar -xvf PhiPack.tar.gz && \ | ||
| cd /PhiPack/src && \ | ||
| make && \ | ||
| cp /PhiPack/Phi /usr/local/bin && \ | ||
| cp /PhiPack/Profile /usr/local/bin | ||
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| # Install HarvestTools | ||
| RUN wget -q https://github.com/marbl/harvest-tools/releases/download/v${HARVEST_VER}/harvesttools-Linux64-v${HARVEST_VER}.tar.gz && \ | ||
| tar -vxf harvesttools-Linux64-v${HARVEST_VER}.tar.gz && \ | ||
| cp harvesttools-Linux64-v${HARVEST_VER}/harvesttools /usr/local/bin/. | ||
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| # Install ParSNP | ||
| RUN wget -q https://github.com/marbl/parsnp/archive/v$PARSNP_VER.tar.gz && \ | ||
| tar -xvf v$PARSNP_VER.tar.gz && \ | ||
| rm v$PARSNP_VER.tar.gz && \ | ||
| cd /parsnp-$PARSNP_VER/muscle && \ | ||
| ./autogen.sh && \ | ||
| ./configure CXXFLAGS='-fopenmp' && \ | ||
| make install && \ | ||
| cd /parsnp-$PARSNP_VER && \ | ||
| ./autogen.sh && \ | ||
| export ORIGIN=\$ORIGIN && \ | ||
| ./configure LDFLAGS='-Wl,-rpath,$$ORIGIN/../muscle/lib' && \ | ||
| make LDADD=-lMUSCLE-3.7 && \ | ||
| make install | ||
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| # install fastani | ||
| RUN wget -q https://github.com/ParBLiSS/FastANI/releases/download/v${FASTANI_VER}/fastANI-Linux64-v${FASTANI_VER}.zip && \ | ||
| unzip fastANI-Linux64-v${FASTANI_VER}.zip -d /usr/local/bin | ||
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| FROM ubuntu:jammy as app | ||
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| ARG PARSNP_VER | ||
| ARG HARVEST_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="ParSNP" | ||
| LABEL software.version="${PARSNP_VER}" | ||
| LABEL description="ParSNP: Rapid core genome multi-alignment." | ||
| LABEL documentation="https://harvest.readthedocs.io/en/latest/content/parsnp.html" | ||
| LABEL website="https://github.com/marbl/parsnp" | ||
| LABEL license="https://github.com/marbl/parsnp/blob/master/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps \ | ||
| python3 \ | ||
| python3-pip \ | ||
| python-is-python3 \ | ||
| unzip \ | ||
| libgomp1 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Copy necessary packages into the production image | ||
| COPY --from=builder /parsnp-$PARSNP_VER/ /parsnp/ | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
| COPY --from=builder /usr/local/lib/* /usr/local/lib/ | ||
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| RUN pip install pyspoa numpy biopython tqdm | ||
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| # Put harvesttools & parsnp in PATH and set LD_LIBRARY_PATH for MUSCLE | ||
| ENV PATH="/parsnp/:$PATH" \ | ||
| LD_LIBRARY_PATH="/usr/local/lib" | ||
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| CMD parsnp -h | ||
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| WORKDIR /data | ||
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| FROM app as test | ||
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| # IS_GITHUB only applicable for tests run by GitHub action | ||
| ARG IS_GITHUB | ||
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| RUN parsnp -h | ||
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| # negative control | ||
| WORKDIR /test/negative | ||
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| RUN mkdir input_dir && \ | ||
| mkdir reference && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/703/365/GCA_000703365.1_Ec2011C-3609/GCA_000703365.1_Ec2011C-3609_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/766/575/GCA_016766575.1_PDT000040717.5/GCA_016766575.1_PDT000040717.5_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/748/565/GCA_000748565.2_ASM74856v2/GCA_000748565.2_ASM74856v2_genomic.fna.gz && \ | ||
| gunzip *.gz && \ | ||
| mv GCA_000703365.1_Ec2011C-3609_genomic.fna reference/. && \ | ||
| mv *fna input_dir && \ | ||
| parsnp -d input_dir -o filter --use-fasttree -v -r reference/GCA_000703365.1_Ec2011C-3609_genomic.fna | ||
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| # positive control | ||
| WORKDIR /test/positive | ||
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| RUN mkdir input_dir && \ | ||
| mkdir reference && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/703/365/GCA_000703365.1_Ec2011C-3609/GCA_000703365.1_Ec2011C-3609_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/766/575/GCA_016766575.1_PDT000040717.5/GCA_016766575.1_PDT000040717.5_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/018/935/GCA_003018935.1_ASM301893v1/GCA_003018935.1_ASM301893v1_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/830/055/GCA_012830055.1_PDT000040719.3/GCA_012830055.1_PDT000040719.3_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/829/335/GCA_012829335.1_PDT000040724.3/GCA_012829335.1_PDT000040724.3_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/018/775/GCA_003018775.1_ASM301877v1/GCA_003018775.1_ASM301877v1_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/829/275/GCA_012829275.1_PDT000040726.3/GCA_012829275.1_PDT000040726.3_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/766/555/GCA_016766555.1_PDT000040728.5/GCA_016766555.1_PDT000040728.5_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/829/195/GCA_012829195.1_PDT000040729.3/GCA_012829195.1_PDT000040729.3_genomic.fna.gz && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/829/295/GCA_012829295.1_PDT000040727.3/GCA_012829295.1_PDT000040727.3_genomic.fna.gz && \ | ||
| gunzip *.gz && \ | ||
| mv GCA_000703365.1_Ec2011C-3609_genomic.fna reference/. && \ | ||
| mv *.fna input_dir/. && \ | ||
| parsnp -d input_dir -o outdir_parsnp_raxml -v -c -r reference/GCA_000703365.1_Ec2011C-3609_genomic.fna && \ | ||
| parsnp -d input_dir -o outdir_parsnp_fasttree --use-fasttree -v -c -r reference/GCA_000703365.1_Ec2011C-3609_genomic.fna && \ | ||
| harvesttools -i outdir_parsnp_fasttree/parsnp.ggr -S outdir_parsnp_fasttree/snp_alignment.txt && \ | ||
| harvesttools -i outdir_parsnp_raxml/parsnp.ggr -S outdir_parsnp_raxml/snp_alignment.txt |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| ## ParSNP | ||
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| This container implements [ParSNP](https://github.com/marbl/parsnp) from the [Harvest suite](https://harvest.readthedocs.io/en/latest/). | ||
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| ### Includes | ||
| - ParSNP: `parsnp` | ||
| - FastTree: `FastTree` or `fasttree` : 2.1.11 | ||
| - RAxML: `raxmlHPC-PTHREADS` : 8.2.12 | ||
| - Mash: `mash` : 2.3 | ||
| - PhiPack: `Phi` : 1.1 | ||
| - HarvestTools: `harvesttools` : 1.3 | ||
| - FastANI: `fastani` : 1.34 | ||
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| ### Requirements | ||
| - [Docker](https://docs.docker.com/get-docker/) | ||
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| ### Running a container | ||
| Pull the image from Docker Hub. | ||
| ``` | ||
| docker pull staphb/parsnp:latest | ||
| ``` | ||
| OR, clone this repository to build & test the image yourself. | ||
| ``` | ||
| git clone [email protected]:StaPH-B/docker-builds.git | ||
| cd docker-builds/parsnp/1.5.6 | ||
| # Run tests | ||
| docker build --target=test -t parsnp-test . | ||
| # Build production image | ||
| docker build --target=app -t parsnp . | ||
| ``` | ||
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| ### Example data analysis | ||
| Set up some input data. | ||
| ``` | ||
| mkdir -p parsnp/input_dir | ||
| cd parsnp/input_dir | ||
| wget \ | ||
| https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/698/515/GCA_000698515.1_CFSAN000661_01.0/GCA_000698515.1_CFSAN000661_01.0_genomic.fna.gz \ | ||
| https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/749/005/GCA_000749005.1_CFSAN000669_01.0/GCA_000749005.1_CFSAN000669_01.0_genomic.fna.gz | ||
| gunzip *.gz | ||
| cd ../ | ||
| ``` | ||
| Run the container to generate a core genome alignment, call SNPs, and build a phylogeny. Output files are written to `output_dir`. | ||
| ``` | ||
| docker run --rm -v $PWD:/data -u $(id -u):$(id -g) staphb/parsnp:latest parsnp \ | ||
| -d input_dir \ | ||
| -o outdir_parsnp \ | ||
| --use-fasttree \ | ||
| -v \ | ||
| -c \ | ||
| -r ! | ||
| ``` |