adds sistr 1.1.2

Author: Kincekara

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/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shigeifinder)](https://hub.docker.com/r/staphb/shigeifinder) | <ul><li>[1.3.2](shigeifinder/1.3.2/)</li><li>[1.3.3](shigeifinder/1.3.3/)</li><li>[1.3.5](shigeifinder/1.3.5/)</li></ul> | https://github.com/LanLab/ShigEiFinder |
 | [Shovill](https://hub.docker.com/r/staphb/shovill/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shovill)](https://hub.docker.com/r/staphb/shovill) | <ul><li>1.0.4</li><li>1.1.0</li></ul> | https://github.com/tseemann/shovill |
 | [Shovill-se](https://hub.docker.com/r/staphb/shovill-se/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shovill-se)](https://hub.docker.com/r/staphb/shovill-se) | <ul><li>1.1.0</li></ul> | https://github.com/rpetit3/shovill/tree/v1.1.0se |
-| [SISTR](https://hub.docker.com/r/staphb/sistr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | <ul><li>1.0.2</li><li>1.1.1</li></ul> | https://github.com/phac-nml/sistr_cmd |
+| [SISTR](https://hub.docker.com/r/staphb/sistr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | <ul><li>1.0.2</li><li>1.1.1</li><li>[1.1.2](./sistr/1.1.2/)</li></ul> | https://github.com/phac-nml/sistr_cmd |
 | [SKA](https://hub.docker.com/r/staphb/ska/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska)](https://hub.docker.com/r/staphb/ska) | <ul><li>1.0</li></ul> | https://github.com/simonrharris/SKA |
 | [SKA2](https://hub.docker.com/r/staphb/ska2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | <ul><li>[0.3.6](./ska2/0.3.6/)</li><li>[0.3.7](./ska2/0.3.7/)</li></ul> | https://github.com/bacpop/ska.rust |
 | [skani](https://github.com/bluenote-1577/skani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/skani) | <ul><li>[0.2.0](./skani/0.2.0)</li><li>[0.2.1](./skani/0.2.1)</li><li>[0.2.2](./skani/0.2.2)</li></ul> | https://github.com/bluenote-1577/skani |

sistr/1.1.2/Dockerfile

@@ -0,0 +1,50 @@
+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 \
+    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
+
+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
+
+RUN 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 

sistr/1.1.2/README.md

@@ -0,0 +1,25 @@
+# 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
+
+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
+```
+