-
Notifications
You must be signed in to change notification settings - Fork 115
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
3 changed files
with
230 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| ARG PARSNP_VER="2.0.5" | ||
| ARG HARVEST_VER="1.3" | ||
|
|
||
| FROM ubuntu:jammy as builder | ||
|
|
||
| ARG PARSNP_VER | ||
| ARG HARVEST_VER | ||
|
|
||
| ARG RAXML_VER="8.2.12" | ||
| ARG FASTTREE_VER="2.1.11" | ||
| ARG MASH_VER="2.3" | ||
| ARG FASTANI_VER="1.34" | ||
|
|
||
| # 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 | ||
|
|
||
| # 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" | ||
|
|
||
| # 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/ | ||
|
|
||
| RUN pip3 install numpy | ||
|
|
||
| # 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 | ||
|
|
||
| # 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 | ||
|
|
||
| # 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${MASH_VER}/* | ||
|
|
||
| # Install PhiPack: https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf | ||
| RUN wget -q https://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar.gz && \ | ||
| tar -xvf PhiPack.tar.gz && \ | ||
| cd /PhiPack/src && \ | ||
| make && \ | ||
| cp /PhiPack/Phi /usr/local/bin && \ | ||
| cp /PhiPack/Profile /usr/local/bin | ||
|
|
||
| # Install HarvestTools | ||
| RUN wget -q https://github.com/marbl/harvest-tools/releases/download/v${HARVEST_VER}/harvesttools-Linux64-v${HARVEST_VER}.tar.gz && \ | ||
| tar -vxf harvesttools-Linux64-v${HARVEST_VER}.tar.gz && \ | ||
| cp harvesttools-Linux64-v${HARVEST_VER}/harvesttools /usr/local/bin/. | ||
|
|
||
| # Install ParSNP | ||
| RUN wget -q https://github.com/marbl/parsnp/archive/v$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 | ||
|
|
||
| # 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${FASTANI_VER}.zip -d /usr/local/bin | ||
|
|
||
| FROM ubuntu:jammy as app | ||
|
|
||
| ARG PARSNP_VER | ||
| ARG HARVEST_VER | ||
|
|
||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="ParSNP" | ||
| LABEL software.version="${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="eriny@utah.gov" | ||
|
|
||
| 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/* | ||
|
|
||
| # Copy necessary packages into the production image | ||
| COPY --from=builder /parsnp-$PARSNP_VER/ /parsnp/ | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin/ | ||
| COPY --from=builder /usr/local/lib/* /usr/local/lib/ | ||
|
|
||
| RUN pip install pyspoa numpy biopython tqdm | ||
|
|
||
| # Put harvesttools & parsnp in PATH and set LD_LIBRARY_PATH for MUSCLE | ||
| ENV PATH="/parsnp/:$PATH" \ | ||
| LD_LIBRARY_PATH="/usr/local/lib" | ||
|
|
||
| CMD parsnp -h | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| FROM app as test | ||
|
|
||
| # IS_GITHUB only applicable for tests run by GitHub action | ||
| ARG IS_GITHUB | ||
|
|
||
| RUN parsnp -h | ||
|
|
||
| # negative control | ||
| WORKDIR /test/negative | ||
|
|
||
| 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 | ||
|
|
||
| # positive control | ||
| WORKDIR /test/positive | ||
|
|
||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| ## ParSNP | ||
|
|
||
| This container implements [ParSNP](https://github.com/marbl/parsnp) from the [Harvest suite](https://harvest.readthedocs.io/en/latest/). | ||
|
|
||
| ### 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 | ||
|
|
||
| ### Requirements | ||
| - [Docker](https://docs.docker.com/get-docker/) | ||
|
|
||
| ### 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 git@github.com: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 . | ||
| ``` | ||
|
|
||
| ### 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 ! | ||
| ``` |