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add pasty 2.1.0
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Kincekara committed Aug 22, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -221,7 +221,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [panqc](https://hub.docker.com/r/staphb/panqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/panqc)](https://hub.docker.com/r/staphb/panqc) | <ul><li>[0.4.0](./panqc/0.4.0/)</li></ul> | https://github.com/maxgmarin/panqc/releases/tag/0.4.0 |
| [parallel-perl](https://hub.docker.com/r/staphb/parallel-perl) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/parallel-perl)](https://hub.docker.com/r/staphb/parallel-perl) | <ul><li>20200722</li></ul> | https://www.gnu.org/software/parallel |
| [parsnp](https://hub.docker.com/r/staphb/parsnp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/parsnp)](https://hub.docker.com/r/staphb/parsnp) | <ul><li>[1.5.6](./parsnp/1.5.6/)</li><li>[2.0.4](./parsnp/2.0.4/)</li><li>[2.0.5](./parsnp/2.0.5/)</li></ul> | https://github.com/marbl/parsnp |
| [pasty](https://hub.docker.com/r/staphb/pasty) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | <ul><li>1.0.2</li><li>[1.0.3](pasty/1.0.3/)</li></ul> | https://github.com/rpetit3/pasty |
| [pasty](https://hub.docker.com/r/staphb/pasty) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | <ul><li>1.0.2</li><li>[1.0.3](pasty/1.0.3/)</li><li>[2.1.0](./pasty/2.1.0/)</li></ul> | https://github.com/rpetit3/pasty |
| [pbmm2](https://hub.docker.com/r/staphb/pbmm2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbmm2)](https://hub.docker.com/r/staphb/pbmm2) | <ul><li>[1.13.1](./pbmm2/1.13.1/)</li></ul> | https://github.com/PacificBiosciences/pbmm2 |
| [Pavian](https://hub.docker.com/r/staphb/pavian) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | <ul><li>[1.2.1](pavian/1.2.1/)</li></ul> | https://github.com/fbreitwieser/pavian |
| [pbptyper](https://hub.docker.com/r/staphb/pbptyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | <ul><li>1.0.0</li><li>1.0.1</li><li>1.0.4</li></ul> | https://github.com/rpetit3/pbptyper |
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50 changes: 50 additions & 0 deletions pasty/2.1.0/Dockerfile
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ARG PASTY_VER="2.1.0"

FROM mambaorg/micromamba:1.5.8 AS app

ARG PASTY_VER

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]"

USER root

RUN apt-get update && apt-get install -y --no-install-recommends \
procps && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN micromamba install --name base -c conda-forge -c bioconda pasty=${PASTY_VER} &&\
micromamba clean -afy

ENV PATH="/opt/conda/bin/:$PATH" \
LC_ALL=C

CMD ["pasty", "--help"]

WORKDIR /data

## Test ##
FROM app AS test

ARG PASTY_VER

RUN apt-get update && apt-get install -y wget

# 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

42 changes: 42 additions & 0 deletions pasty/2.1.0/README.md
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# pasty container

Main tool : [pasty](https://github.com/rpetit3/pasty)

Additional tools:

- camlhmp 1.0.0
- blast 2.16.0+

Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty)

A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies

## Example Usage

```bash
pasty --input ./data/O1-GCF_001420225.fna.gz --prefix O1-GCF_001420225 --outdir results/

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

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
```

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