diff --git a/README.md b/README.md index ecf9c9954..4ebd7aa4d 100644 --- a/README.md +++ b/README.md @@ -269,7 +269,7 @@ To learn more about the docker pull rate limits and the open source software pro | [ShigEiFinder](https://hub.docker.com/r/staphb/shigeifinder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/shigeifinder)](https://hub.docker.com/r/staphb/shigeifinder) | | https://github.com/LanLab/ShigEiFinder | | [Shovill](https://hub.docker.com/r/staphb/shovill/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/shovill)](https://hub.docker.com/r/staphb/shovill) | | https://github.com/tseemann/shovill | | [Shovill-se](https://hub.docker.com/r/staphb/shovill-se/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/shovill-se)](https://hub.docker.com/r/staphb/shovill-se) | | https://github.com/rpetit3/shovill/tree/v1.1.0se | -| [SISTR](https://hub.docker.com/r/staphb/sistr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | | https://github.com/phac-nml/sistr_cmd | +| [SISTR](https://hub.docker.com/r/staphb/sistr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | | https://github.com/phac-nml/sistr_cmd | | [SKA](https://hub.docker.com/r/staphb/ska/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ska)](https://hub.docker.com/r/staphb/ska) | | https://github.com/simonrharris/SKA | | [SKA2](https://hub.docker.com/r/staphb/ska2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | | https://github.com/bacpop/ska.rust | | [skani](https://github.com/bluenote-1577/skani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/skani) | | https://github.com/bluenote-1577/skani | diff --git a/sistr/1.1.2/Dockerfile b/sistr/1.1.2/Dockerfile new file mode 100644 index 000000000..25ed8a6e6 --- /dev/null +++ b/sistr/1.1.2/Dockerfile @@ -0,0 +1,56 @@ +FROM ubuntu:jammy AS app + +ARG SISTR_VER="1.1.2" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="SISTR" +LABEL software.version="1.1.2" +LABEL description="Salmonella In Silico Typing Resource (SISTR)" +LABEL website="https://github.com/peterk87/sistr_cmd" +LABEL license="https://github.com/peterk87/sistr_cmd/blob/master/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +ARG DEBIAN_FRONTEND=noninteractive + +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + ca-certificates \ + python3-setuptools \ + python3-pandas \ + python3-numpy \ + python3-tables \ + python3-scipy \ + python3-pycurl \ + python3-fastcluster \ + ncbi-blast+ \ + mafft \ + mash &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget https://github.com/phac-nml/sistr_cmd/archive/refs/tags/v${SISTR_VER}.tar.gz &&\ + tar -xvf v${SISTR_VER}.tar.gz && rm v${SISTR_VER}.tar.gz &&\ + cd sistr_cmd-${SISTR_VER}/ &&\ + python3 setup.py install &&\ + cd .. && rm -rf sistr_cmd-${SISTR_VER} + +WORKDIR /data + +ENV LC_ALL=C + +CMD ["sistr", "--help"] + +## Test ## +FROM app AS test + +# Testing Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 str. 00-0163 SES60163_1000002 +RUN wget -q https://github.com/phac-nml/sistr_cmd/raw/master/tests/00_0163.fasta &&\ + sistr --qc -vv --alleles-output 00_0163.allele-results.json --novel-alleles 00_0163.novel-alleles.fasta --cgmlst-profiles 00_0163.cgmlst-profiles.csv -f tab -o 00_0163.sistr-output.tab 00_0163.fasta &&\ + cat 00_0163.sistr-output.tab + +# Testing Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006945.2/) +RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz &&\ + gunzip GCF_000006945.2_ASM694v2_genomic.fna.gz &&\ + sistr --qc -vv --alleles-output allele-results.json --novel-alleles novel-alleles.fasta --cgmlst-profiles cgmlst-profiles.csv -f tab -o sistr-output.tab GCF_000006945.2_ASM694v2_genomic.fna &&\ + cat sistr-output.tab \ No newline at end of file diff --git a/sistr/1.1.2/README.md b/sistr/1.1.2/README.md new file mode 100644 index 000000000..59d58a151 --- /dev/null +++ b/sistr/1.1.2/README.md @@ -0,0 +1,27 @@ +# SISTR container + +Main tool: [sistr](https://github.com/phac-nml/sistr_cmd) + +Code repository: https://github.com/phac-nml/sistr_cmd + +Additional tools: +- blast : 2.12.0+ +- mafft : v7.490 +- mash : 2.3 +- pandas : 1.3.5 +- numpy : 1.21.5 + +Basic information on how to use this tool: +- executable: sistr +- help: -h, --help +- version: -V, --version +- description: (Salmonella In Silico Typing Resource) Command-line Tool + +Full documentation: https://github.com/phac-nml/sistr_cmd + +## Example Usage + +```bash +sistr --qc -vv --alleles-output allele-results.json --novel-alleles novel-alleles.fasta --cgmlst-profiles cgmlst-profiles.csv -f tab -o sistr-output.tab genome.fasta +``` +