diff --git a/README.md b/README.md index aee45fdda..6276720d1 100644 --- a/README.md +++ b/README.md @@ -307,7 +307,7 @@ To learn more about the docker pull rate limits and the open source software pro | [snp-dists](https://hub.docker.com/r/staphb/snp-dists)
[![docker pulls](https://badgen.net/docker/pulls/staphb/snp-dists)](https://hub.docker.com/r/staphb/snp-dists) | | https://github.com/tseemann/snp-dists | | [SNP-sites](https://hub.docker.com/r/staphb/snp-sites)
[![docker pulls](https://badgen.net/docker/pulls/staphb/snp-sites)](https://hub.docker.com/r/staphb/snp-sites) | | https://github.com/sanger-pathogens/snp-sites | | [SNVPhyl-tools](https://hub.docker.com/r/staphb/snvphyl-tools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/snvphyl-tools)](https://hub.docker.com/r/staphb/snvphyl-tools) | | https://github.com/phac-nml/snvphyl-tools | -| [SPAdes](https://hub.docker.com/r/staphb/spades/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/spades)](https://hub.docker.com/r/staphb/spades) | | https://github.com/ablab/spades
http://cab.spbu.ru/software/spades/ | +| [SPAdes](https://hub.docker.com/r/staphb/spades/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/spades)](https://hub.docker.com/r/staphb/spades) | | https://github.com/ablab/spades
http://cab.spbu.ru/software/spades/ | | [SRA-toolkit](https://hub.docker.com/r/staphb/sratoolkit/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sratoolkit)](https://hub.docker.com/r/staphb/sratoolkit) | | https://github.com/ncbi/sra-tools | | [SRST2](https://hub.docker.com/r/staphb/srst2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/srst2)](https://hub.docker.com/r/staphb/srst2) | | https://github.com/katholt/srst2 | | [Staramr](https://hub.docker.com/r/staphb/staramr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/staramr)](https://hub.docker.com/r/staphb/staramr) | | https://github.com/phac-nml/staramr | diff --git a/build-files/spades/4.1.0/Dockerfile b/build-files/spades/4.1.0/Dockerfile new file mode 100644 index 000000000..f40842b04 --- /dev/null +++ b/build-files/spades/4.1.0/Dockerfile @@ -0,0 +1,57 @@ +FROM ubuntu:jammy AS app + +# to make it easier to upgrade for new versions; ARG variables only persist during docker image build time +ARG SPADES_VER="4.1.0" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="SPAdes" +LABEL software.version="${SPADES_VER}" +LABEL description="de novo DBG genome assembler" +LABEL website="https://github.com/ablab/spades" +LABEL license="https://github.com/ablab/spades/blob/main/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" + +# install dependencies; cleanup apt garbage +# python v3.8.10 is installed here; point 'python' to python3 +RUN apt-get update && apt-get install --no-install-recommends -y \ + python3 \ + python3-distutils \ + wget \ + pigz \ + ca-certificates \ + libgomp1 && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* && \ + update-alternatives --install /usr/bin/python python /usr/bin/python3 10 + +# install SPAdes binary; make /data +RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VER}/SPAdes-${SPADES_VER}-Linux.tar.gz && \ + tar -xzf SPAdes-${SPADES_VER}-Linux.tar.gz && \ + rm -r SPAdes-${SPADES_VER}-Linux.tar.gz && \ + mkdir /data + +# set PATH and locale settings for singularity +ENV LC_ALL=C.UTF-8 \ + PATH="${PATH}:/SPAdes-${SPADES_VER}-Linux/bin" + +CMD ["spades.py", "--help"] + +WORKDIR /data + +# test layer +FROM app AS test + +# print version and run the supplied test flag +RUN spades.py --version && spades.py --help + +# run the supplied test +RUN spades.py --test + +WORKDIR /test + +# run on some test files +RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_1.fastq.gz && \ + wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR323/020/SRR32343420/SRR32343420_2.fastq.gz && \ + spades.py --isolate -1 SRR32343420_1.fastq.gz -2 SRR32343420_2.fastq.gz --threads 4 -o test && \ + head /test/test/contigs.fasta diff --git a/build-files/spades/4.1.0/README.md b/build-files/spades/4.1.0/README.md new file mode 100644 index 000000000..cacd13cc8 --- /dev/null +++ b/build-files/spades/4.1.0/README.md @@ -0,0 +1,22 @@ +# SPAdes + +Main tool: [SPAdes](https://github.com/ablab/spades) + +SPAdes genome assembler + +## Example commands + +```bash +# Test with supplied E. coli data +docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --test + +# paired-end Illumina reads are in the $PWD +$ ls +SRR7062227_1.fastq.gz SRR7062227_2.fastq.gz + +# assemble with your own data (broken into two lines for readability) +docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest \ + spades.py -1 /data/SRR7062227_1.fastq.gz -2 /data/SRR7062227_2.fastq.gz -t 8 --isolate -o /data/SRR7062227-spades-output/ +``` + +View full `spades` help options: `docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --help`