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ARG PASTY_VER="2.1.0" | ||
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FROM mambaorg/micromamba:1.5.8 AS app | ||
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ARG PASTY_VER | ||
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LABEL base.image="mambaorg/micromamba:1.5.8" | ||
LABEL dockerfile.version="1" | ||
LABEL software="pasty" | ||
LABEL software.version="${PASTY_VERSION}" | ||
LABEL description="In silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies" | ||
LABEL website="https://github.com/rpetit3/pasty" | ||
LABEL license="https://github.com/rpetit3/pasty/blob/main/LICENSE" | ||
LABEL maintainer="Curtis Kapsak" | ||
LABEL maintainer.email="[email protected]" | ||
LABEL maintainer2="Kutluhan Incekara" | ||
LABEL maintainer2.email="[email protected]" | ||
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USER root | ||
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RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
procps && \ | ||
apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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RUN micromamba install --name base -c conda-forge -c bioconda pasty=${PASTY_VER} &&\ | ||
micromamba clean -afy | ||
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ENV PATH="/opt/conda/bin/:$PATH" \ | ||
LC_ALL=C | ||
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CMD ["pasty", "--help"] | ||
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WORKDIR /data | ||
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## Test ## | ||
FROM app AS test | ||
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ARG PASTY_VER | ||
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RUN apt-get update && apt-get install -y wget | ||
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# adapted from https://github.com/rpetit3/pasty/blob/main/test/README.md | ||
RUN wget -q https://github.com/rpetit3/pasty/archive/refs/tags/v${PASTY_VER}.tar.gz &&\ | ||
tar -xvf v${PASTY_VER}.tar.gz &&\ | ||
cd pasty-${PASTY_VER}/test/ &&\ | ||
for i in $(ls data | grep "fna.gz"); do pasty --input ./data/$i --prefix $(basename $i .fna.gz) --outdir results/ --force; done &&\ | ||
head -n 1 results/O1-GCF_001420225.tsv > staphb-test.tsv &&\ | ||
ls results/ | grep -v "details" | grep -v "blastn" | xargs -I {} grep -v "schema_version" results/{} | sort -k1 >> staphb-test.tsv &&\ | ||
cat staphb-test.tsv | ||
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# pasty container | ||
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Main tool : [pasty](https://github.com/rpetit3/pasty) | ||
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Additional tools: | ||
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- camlhmp 1.0.0 | ||
- blast 2.16.0+ | ||
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Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty) | ||
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A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies | ||
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## Example Usage | ||
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```bash | ||
pasty --input ./data/O1-GCF_001420225.fna.gz --prefix O1-GCF_001420225 --outdir results/ | ||
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Running camlhmp with following parameters: | ||
--input ./data/O1-GCF_001420225.fna.gz | ||
--yaml /opt/conda/bin/../share/pasty/pa-osa.yaml | ||
--targets /opt/conda/bin/../share/pasty/pa-osa.fasta | ||
--outdir results/ | ||
--prefix O1-GCF_001420225 | ||
--min-pident 95 | ||
--min-coverage 95 | ||
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Starting camlhmp for P. aeruginosa serogrouping... | ||
Running blastn... | ||
Processing hits... | ||
Final Results... | ||
P. aeruginosa serogrouping | ||
┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┓ | ||
┃ sample ┃ type ┃ targets ┃ coverages ┃ hits ┃ schema ┃ schema_version ┃ camlhmp_version ┃ params ┃ comment ┃ | ||
┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━┩ | ||
│ O1-GCF_001420225 │ O1 │ O1 │ 100.00 │ 1 │ pasty │ 2.1.0 │ 1.0.0 │ min-coverage=95;min-pident=95 │ │ | ||
└──────────────────┴──────┴─────────┴───────────┴──────┴────────┴────────────────┴─────────────────┴───────────────────────────────┴─────────┘ | ||
Writing outputs... | ||
Final predicted type written to results/O1-GCF_001420225.tsv | ||
Results against each type written to results/O1-GCF_001420225.details.tsv | ||
blastn results written to results/O1-GCF_001420225.blastn.tsv | ||
``` |