diff --git a/Program_Licenses.md b/Program_Licenses.md index b7d94ef87..b8b299832 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -109,6 +109,7 @@ The licenses of the open-source software that is contained in these Docker image | OrthoFinder | GNU GPLv3 | https://github.com/davidemms/OrthoFinder/blob/master/License.md | | Panaroo | MIT | https://github.com/gtonkinhill/panaroo/blob/master/LICENSE | | Pangolin | GNU GPLv3 | https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt | +| Parsnp | Battelle National Biodefense Institute (BNBI) | https://github.com/marbl/parsnp?tab=License-1-ov-file#readme | | pasty | Apache 2.0 | https://github.com/rpetit3/pasty/blob/main/LICENSE | | Pavian | GNU GPLv3 | https://github.com/fbreitwieser/pavian/blob/master/DESCRIPTION | | pbptyper | MIT | https://github.com/rpetit3/pbptyper/blob/main/LICENSE | diff --git a/README.md b/README.md index c15d583ea..e70c33a5b 100644 --- a/README.md +++ b/README.md @@ -213,6 +213,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | (https://hub.docker.com/r/staphb/panaroo) | | [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) |
Click to see Pangolin v4.2 and older versions! **Pangolin version & pangoLEARN data release date** **Pangolin version & pangolin-data version**
**Pangolin version & pangolin-data version** | https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) | | [parallel-perl](https://hub.docker.com/r/staphb/parallel-perl)
[![docker pulls](https://badgen.net/docker/pulls/staphb/parallel-perl)](https://hub.docker.com/r/staphb/parallel-perl) | | https://www.gnu.org/software/parallel | +| [parsnp](https://hub.docker.com/r/staphb/parsnp)
[![docker pulls](https://badgen.net/docker/pulls/staphb/parsnp)](https://hub.docker.com/r/staphb/parsnp) | | https://github.com/marbl/parsnp | | [pasty](https://hub.docker.com/r/staphb/pasty)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | | https://github.com/rpetit3/pasty | | [Pavian](https://hub.docker.com/r/staphb/pavian)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | | https://github.com/fbreitwieser/pavian | | [pbptyper](https://hub.docker.com/r/staphb/pbptyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | | https://github.com/rpetit3/pbptyper | diff --git a/parsnp/2.0.4/Dockerfile b/parsnp/2.0.4/Dockerfile new file mode 100644 index 000000000..d017e06dc --- /dev/null +++ b/parsnp/2.0.4/Dockerfile @@ -0,0 +1,177 @@ +ARG PARSNP_VER="2.0.4" +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 diff --git a/parsnp/2.0.4/README.md b/parsnp/2.0.4/README.md new file mode 100644 index 000000000..cfd25e1e0 --- /dev/null +++ b/parsnp/2.0.4/README.md @@ -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 ! +```