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* shigapass * update license info * update shigapass * fixing permissions and updating Readme * correct relative path to shigapass readme * Update shigapass README.md to list blast dependency --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| FROM ubuntu:jammy as app | ||
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| # List all software versions are ARGs near the top of the dockerfile | ||
| ARG SHIGAPASS_VER=1.5.0 | ||
| ARG BLAST_VER=2.12.0 | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="ShigaPass" | ||
| LABEL software.version="${SHIGAPASS_VER}" | ||
| LABEL description="In silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes." | ||
| LABEL website="https://github.com/imanyass/ShigaPass/" | ||
| LABEL license="https://github.com/imanyass/ShigaPass/blob/main/LICENSE" | ||
| LABEL maintainer="Jill Hagey" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| git \ | ||
| libgomp1 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # install ncbi-blast+ 2.12.0 pre-compiled linux binaries | ||
| ARG BLAST_VER=2.12.0 | ||
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| #creating variable for referencing database | ||
| ENV DB_PATH=/ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass_DataBases/ | ||
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| RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VER}/ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \ | ||
| tar -xzf ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \ | ||
| rm ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz | ||
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| # install Shigapass | ||
| RUN wget https://github.com/imanyass/ShigaPass/archive/refs/tags/v${SHIGAPASS_VER}.tar.gz && \ | ||
| tar -xzf v${SHIGAPASS_VER}.tar.gz && \ | ||
| rm -r v${SHIGAPASS_VER}.tar.gz && \ | ||
| chmod +x /ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass.sh && \ | ||
| chmod -R a+rw ${DB_PATH} && \ | ||
| mkdir /data | ||
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| # 'ENV' instructions set environment variables that persist from the build into the resulting image | ||
| # Use for e.g. $PATH and locale settings for compatibility with Singularity | ||
| ENV PATH="/ncbi-blast-${BLAST_VER}+/bin/:/ShigaPass-${SHIGAPASS_VER}/SCRIPT:$PATH" \ | ||
| LC_ALL=C | ||
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| #creating variable for referencing database | ||
| ENV DB_PATH=/ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass_DataBases/ | ||
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| # running test to index the database | ||
| RUN gunzip /ShigaPass-${SHIGAPASS_VER}/Example/Input/*.gz && \ | ||
| sed -i "s/^/\/ShigaPass-${SHIGAPASS_VER}\//" /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt && \ | ||
| ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p ${DB_PATH} -u | ||
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| # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' | ||
| CMD [ "ShigaPass.sh" ] | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| # A second FROM insruction creates a new stage | ||
| FROM app as test | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| ## print help and version info to ensure ShigaPass is in path and is executable | ||
| RUN ShigaPass.sh -h && \ | ||
| ShigaPass.sh -v | ||
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| # Testing a script - need to unzip the test files and correct the path for the container | ||
| RUN ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p ${DB_PATH} |
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| # ShigaPass container | ||
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| Main tool: [ShigaPass](https://github.com/imanyass/ShigaPass) | ||
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| Code repository: https://github.com/imanyass/ShigaPass | ||
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| Additional tools: | ||
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| - ncbi-blast+ 2.12.0 | ||
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| Basic information on how to use this tool: | ||
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| ```` | ||
| ###### This tool is used to predict Shigella serotypes ##### | ||
| Usage : ShigaPass.sh [options] | ||
| options : | ||
| -l List of input file(s) (FASTA) with their path(s) (mandatory) | ||
| -o Output directory (mandatory) | ||
| -p Path to databases directory (mandatory) | ||
| -t Number of threads (optional, default: 2) | ||
| -u Call the makeblastdb utility for databases initialisation (optional, but required when running the script for the first time) | ||
| -k Do not remove subdirectories (optional) | ||
| -v Display the version and exit | ||
| -h Display this help and exit | ||
| Example: ShigaPass.sh -l list_of_fasta.txt -o ShigaPass_Results -p ShigaPass/ShigaPass_DataBases -t 4 -u -k | ||
| Please note that the -u option should be used when running the script for the first time and after databases updates | ||
| ```` | ||
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| > ShigaPass is a new in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes. | ||
| Additional information: | ||
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| Full documentation: https://github.com/imanyass/ShigaPass | ||
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| Included Database: Found at `/ShigaPass-${version}/SCRIPT/ShigaPass_DataBases/` so for v1.5.0 use `-p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/`. This database has already been indexed so there is no need to pass `-u` with your command. If you do a permissions error will occur. | ||
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| ## Example Usage | ||
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| ```bash | ||
| ShigaPass.sh -l ShigaPass_test.txt -o ShigaPass_Results -p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/ | ||
| ``` |